2QS3 | pdb_00002qs3

Crystal structure of the GluR5 ligand binding core dimer in complex with UBP316 at 1.76 Angstroms resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F34	pdb entry 2F34

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.8	293	18% PEG 1K, 100mM Tris-Cl, 2.5mM UBP316, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.766	α = 90
b = 97.702	β = 90
c = 128.604	γ = 90

Symmetry
Space Group	C 2 2 21

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	MARMOSAIC 300 mm CCD		2006-11-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.0000	APS	22-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	1.76	40	98.2	0.037	13.8	5.3	61223	61223	1	1	24.47

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	1.76	1.82	98.6		0.381	4	5.3

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-Factor (All)	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	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 2F34	1.76	32.22	57079	57079	3022	98.27	0.18897	0.18897	0.18746	0.19	0.21814	0.22	RANDOM	30.78

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.055
r_dihedral_angle_3_deg	13.698
r_dihedral_angle_4_deg	13.307
r_dihedral_angle_1_deg	5.013
r_scangle_it	1.896
r_scbond_it	1.219
r_angle_refined_deg	1.185
r_mcangle_it	0.872
r_mcbond_it	0.515
r_nbtor_refined	0.297

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.055
r_dihedral_angle_3_deg	13.698
r_dihedral_angle_4_deg	13.307
r_dihedral_angle_1_deg	5.013
r_scangle_it	1.896
r_scbond_it	1.219
r_angle_refined_deg	1.185
r_mcangle_it	0.872
r_mcbond_it	0.515
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.183
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.105
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4014
Nucleic Acid Atoms
Solvent Atoms	409
Heterogen Atoms	94

Software

Software
Software Name	Purpose
REFMAC	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	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.