4LZ5 | pdb_00004lz5

Crystal structures of GLuR2 ligand-binding-domain in complex with glutamate and positive allosteric modulators

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LBC	PDB ENTRY 1LBC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	1 uL 7 mg/mL protein in 10 mM (S)-Glu, 10 mM HEPES, pH 7.5, 20 mM sodium chloride, 1 mM EDTA, 150 uM ligand (from 30 mM DMSO stock) + 1 uL reservoir (10% PEG8000, 0.1 M zinc acetate, 0.1 M sodium acetate, pH 5.5), crystals appeared in 3-5 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.46	50.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 114.751	α = 90
b = 164.541	β = 90
c = 47.46	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 17-ID	1.00	APS	17-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.5	94.072	98.3	0.071	14.7	6.1		141715		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.55	87.8		0.305		3.1	12503

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 1LBC	1.5	94.07	141629	7111	98.13	0.1708	0.169	0.18	0.203	0.21	RANDOM	20.4257

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]
0.11			0.08		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.609
r_dihedral_angle_4_deg	20.099
r_dihedral_angle_3_deg	13.313
r_dihedral_angle_1_deg	6.303
r_scangle_it	5.855
r_scbond_it	4.123
r_mcangle_it	2.811
r_angle_refined_deg	2.676
r_mcbond_it	2.233
r_angle_other_deg	1.231
r_mcbond_other	0.576
r_xyhbond_nbd_other	0.323
r_nbd_refined	0.283
r_metal_ion_refined	0.258
r_symmetry_vdw_refined	0.251
r_nbd_other	0.215
r_xyhbond_nbd_refined	0.211
r_symmetry_vdw_other	0.205
r_nbtor_refined	0.189
r_symmetry_hbond_refined	0.189
r_chiral_restr	0.17
r_nbtor_other	0.097
r_symmetry_metal_ion_refined	0.056
r_bond_refined_d	0.035
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6035
Nucleic Acid Atoms
Solvent Atoms	1263
Heterogen Atoms	83

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction