7LZ1 | pdb_00007lz1

Structure of glutamate receptor-like channel GLR3.4 ligand-binding domain in complex with serine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7LZ0	PDB entry 7LZ0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION		277	2 M ammonium sulfate

Crystal Properties
Matthews coefficient	Solvent content
2.45	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.509	α = 90
b = 74.509	β = 90
c = 507.975	γ = 120

Symmetry
Space Group	P 65 2 2

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 PILATUS 6M-F		2020-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97918	APS	24-ID-C

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	1.51	72.57	100	0.086	0.089	0.023	0.999	15.4	15.2		133111

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	1.51	1.54	100		1.486	1.541	0.404	0.524		14.3

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	PDB entry 7LZ0	1.51	64.61	126247	6610	99.98	0.2038	0.2023	0.21	0.2323	0.24	RANDOM	26.481

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]
0.23	0.11		0.23		-0.74

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.332
r_dihedral_angle_3_deg	14.083
r_dihedral_angle_4_deg	13.977
r_dihedral_angle_1_deg	7.355
r_angle_refined_deg	1.718
r_angle_other_deg	1.445
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.332
r_dihedral_angle_3_deg	14.083
r_dihedral_angle_4_deg	13.977
r_dihedral_angle_1_deg	7.355
r_angle_refined_deg	1.718
r_angle_other_deg	1.445
r_chiral_restr	0.087
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5862
Nucleic Acid Atoms
Solvent Atoms	205
Heterogen Atoms	42

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
PHASER	phasing
PDB_EXTRACT	data extraction
Aimless	data scaling

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.