3GBB | pdb_00003gbb

X-ray structure of iGluR5 ligand-binding core (S1S2) in complex with MSVIII-19 at 2.10A resolution

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	280	PEG4000, LiSO4, phosphate-citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.28	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.9	α = 100.89
b = 45.12	β = 92.31
c = 66.98	γ = 94.65

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MAR CCD 165 mm		2006-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MAX II BEAMLINE I911-2	1.043	MAX II	I911-2

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	2.1	65.668	96.4	0.081	0.081	8.511	2.2	28932	28932			12.2

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)
	2.1	2.21	94.5		0.271	0.271	2.8	2.2	4160

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1YCJ	2.1	29.28	28925	28925	1452	96.3	0.201	0.19	0.251	0.24	Random	23.3

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]
6.28	0.43	-7.2	-6.77	-0.38	0.49

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	22
c_scangle_it	3.215
c_mcangle_it	2.293
c_scbond_it	2.174
c_mcbond_it	1.421
c_angle_deg	1.243
c_improper_angle_d	0.98
c_bond_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4123
Nucleic Acid Atoms
Solvent Atoms	346
Heterogen Atoms	36

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
xia2	data reduction
xia2	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.