2QS2 | pdb_00002qs2

Crystal structure of the GluR5 ligand binding core dimer in complex with UBP318 at 1.80 Angstroms resolution

X-RAY DIFFRACTION

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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	285	21% PEG 1K, 100mM Tris-Cl, 2.5mM UBP318, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.59

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.124	α = 90
b = 98.176	β = 90
c = 128.594	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	0.91915	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	1.8	40	93.7	0.048	14.2	7.4	58102	58102	1	1	23.05

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	1.8	1.86	96.2		0.338	5.22	7.2

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-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	pdb entry 2F34	1.8	32.29	51350	51350	2715	93.71	0.19264	0.19264	0.19129	0.21869	0.2579	RANDOM	29.225

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	34.209
r_dihedral_angle_4_deg	16.681
r_dihedral_angle_3_deg	13.7
r_dihedral_angle_1_deg	5.089
r_scangle_it	1.963
r_scbond_it	1.38
r_angle_refined_deg	1.179
r_mcangle_it	0.904
r_mcbond_it	0.554
r_nbtor_refined	0.297
r_symmetry_vdw_refined	0.21
r_nbd_refined	0.185
r_xyhbond_nbd_refined	0.12
r_symmetry_hbond_refined	0.112
r_chiral_restr	0.077
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	413
Heterogen Atoms	82

Software

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