3H6U | pdb_00003h6u

Crystal structure of the iGluR2 ligand-binding core (S1S2J-N754S) in complex with glutamate and NS1493 at 1.85 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M5C	PDB ENTRY 1M5C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.5	279	25 % PEG 8000, 0.1 M Lithium sulfate, 0.1 M Phosphate-citrate pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 279K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.462	α = 90
b = 64.086	β = 90
c = 47.272	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	MARRESEARCH		2006-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11		EMBL/DESY, HAMBURG	X11

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	1.85	19.47	98.7	0.058	33.1	7.9		24228			21

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	1.85	1.92	91.6		0.419	0.419	5.2	7.9

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	DIFFERENCE FOURIER	THROUGHOUT	PDB ENTRY 1M5C	1.85	19.47	23457	1177	99.4	0.181	0.181	0.18	0.215	0.18	RANDOM	24.8

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]
-11.136			4.687		6.449

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.9
c_scangle_it	3.14
c_scbond_it	2.111
c_mcangle_it	1.814
c_mcbond_it	1.232
c_angle_deg	1.21
c_improper_angle_d	0.71
c_bond_d	0.005
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2037
Nucleic Acid Atoms
Solvent Atoms	384
Heterogen Atoms	93

Software

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