3H6W | pdb_00003h6w

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS5217 at 1.50 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FTJ	PDB entry 1FTJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	279	20 % PEG 4000, 0.1 M Ammonium sulfate, 0.1 M Cacodylate pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 47.01	α = 90
b = 47.179	β = 91.88
c = 118.412	γ = 90

Symmetry
Space Group	P 1 2 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	CCD	MAR CCD 165 mm		2006-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8080	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.49	17.38	85.6	0.041	0.041	25.2	3.7		72325			18

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.55	95.4		0.405	0.405	2.6		8047

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-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 1FTJ	1.49	17.38	71603	1392	84.51	0.189	0.19	0.232	0.24	RANDOM	19.9

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]
0.76		0.84	-1.33		0.62

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.659
r_dihedral_angle_4_deg	21.63
r_dihedral_angle_3_deg	13.571
r_dihedral_angle_1_deg	5.768
r_sphericity_free	4.937
r_scangle_it	2.987
r_scbond_it	2.235
r_sphericity_bonded	2.065
r_mcangle_it	1.44
r_angle_refined_deg	1.36
r_mcbond_it	1.202
r_rigid_bond_restr	1.153
r_angle_other_deg	0.872
r_mcbond_other	0.39
r_nbd_refined	0.213
r_nbd_other	0.19
r_nbtor_refined	0.182
r_symmetry_vdw_other	0.182
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.131
r_symmetry_vdw_refined	0.125
r_nbtor_other	0.09
r_chiral_restr	0.079
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4081
Nucleic Acid Atoms
Solvent Atoms	683
Heterogen Atoms	96

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection