6ZBV

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody Sb_GlyT1#7

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	LIPIDIC CUBIC PHASE	7	292.75	0.1M ADA pH 7, 13-25% PEG600, 4-14% v/v-1,3-Butanediol

Crystal Properties
Matthews coefficient	Solvent content
2.92	57.89

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.17	α = 90
b = 58.14	β = 100.38
c = 122.31	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	2019-10-05	M	SINGLE WAVELENGTH
2	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-10-04	M	SINGLE WAVELENGTH
3	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-09-21	M	SINGLE WAVELENGTH
4	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-09-19	M	SINGLE WAVELENGTH
5	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-08-07	M	SINGLE WAVELENGTH
6	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-08-06	M	SINGLE WAVELENGTH
7	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-07-14	M	SINGLE WAVELENGTH
8	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M	Mirrors	2019-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
2	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
3	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
4	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
5	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
6	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
7	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)
8	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)	0.9801	PETRA III, EMBL c/o DESY	P14 (MX2)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	3.4	30	99.71	0.42	0.44	0.1225	0.985	6.57	12.1		12641			103.12

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.4	3.5	100		2.688	2.809	0.7956	0.541	1.69	11.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4us3, 6dzz	3.4	29.67	12641	633	99.9	0.2166	0.2144	0.2585	RANDOM	113.5

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]
-3.7653		17.4019	3.4775		0.2879

RMS Deviations
Key	Refinement Restraint Deviation
t_other_torsion	13.87
t_omega_torsion	4.82
t_angle_deg	1.07
t_bond_d	0.009
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	13.87
t_omega_torsion	4.82
t_angle_deg	1.07
t_bond_d	0.009
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	5222
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	61

Software

Software
Software Name	Purpose
BUSTER	refinement
XDS	data reduction
PDB_EXTRACT	data extraction
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 R01GM133198.