6ZPL | pdb_00006zpl

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4US3	4us3, 6dzz
experimental model	PDB	6DZZ	4us3, 6dzz

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	7	292.75	Crystals appeared in 3-10 days in 0.1 M ADA pH 7, 13-25% PEG600, 4-14% v/v, 1,3-Butanediol with the longest dimension of 2-5 um.

Crystal Properties
Matthews coefficient	Solvent content
3.24	61.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.41	α = 90
b = 69.71	β = 92.86
c = 149.43	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-20	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-17	M	SINGLE WAVELENGTH
3	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-16	M	SINGLE WAVELENGTH
4	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-13	M	SINGLE WAVELENGTH
5	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-09	M	SINGLE WAVELENGTH
6	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-08	M	SINGLE WAVELENGTH
7	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-05	M	SINGLE WAVELENGTH
8	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-04	M	SINGLE WAVELENGTH
9	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-02	M	SINGLE WAVELENGTH
10	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-12-01	M	SINGLE WAVELENGTH
11	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-11-29	M	SINGLE WAVELENGTH
12	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-11-28	M	SINGLE WAVELENGTH
13	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-11-20	M	SINGLE WAVELENGTH
14	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-11-06	M	SINGLE WAVELENGTH
15	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-10-23	M	SINGLE WAVELENGTH
16	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-09-24	M	SINGLE WAVELENGTH
17	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-09-02	M	SINGLE WAVELENGTH
18	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-07-13	M	SINGLE WAVELENGTH
19	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-07-12	M	SINGLE WAVELENGTH
20	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-06-12	M	SINGLE WAVELENGTH
21	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2018-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
2	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
3	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
4	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
5	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
6	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
7	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
8	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
9	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
10	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
11	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
12	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
13	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
14	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
15	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
16	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
17	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
18	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
19	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
20	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)
21	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.98	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	3.9	29.86	99.61	0.9253	0.2571	0.982	4.39	12.6		22222			101.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.9	4.039	100		0.276	1.13	12

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4us3, 6dzz	3.945	29.07	21462	1072	100	0.2774	0.2766	0.32	0.2914	0.34	RANDOM	106.35

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
9.39		0.981	-27.8287		18.4387

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.66
t_omega_torsion	3.97
t_angle_deg	0.94
t_bond_d	0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	15.66
t_omega_torsion	3.97
t_angle_deg	0.94
t_bond_d	0.007
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12413
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	126

Software

Software
Software Name	Purpose
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 6ZPL | pdb_00006zpl

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.

Starting Model(s)

Crystallization

Crystal Data

Diffraction

Data Collection

Refinement

Software

6ZPL | pdb_00006zpl