2OR4

A high resolution crystal structure of human glutamate carboxypeptidase II in complex with quisqualic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2OOTPDB ENTRY 2OOT

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 13% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.3262.95

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.007α = 90
b = 130.437β = 90
c = 159.508γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 225 mm2006-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0000APS22-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.625096.70.0728.211129603129603-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.621.6874.80.4652.75.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONRigid bodyTHROUGHOUTPDB ENTRY 2OOT1.6230123053652196.590.185930.18420.21908RANDOM27.218
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]
0.94-1.850.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.264
r_dihedral_angle_3_deg14.406
r_dihedral_angle_4_deg13.007
r_sphericity_free7.115
r_dihedral_angle_1_deg5.774
r_scangle_it3.989
r_scbond_it2.681
r_angle_refined_deg1.939
r_mcangle_it1.797
r_mcbond_it1.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.264
r_dihedral_angle_3_deg14.406
r_dihedral_angle_4_deg13.007
r_sphericity_free7.115
r_dihedral_angle_1_deg5.774
r_scangle_it3.989
r_scbond_it2.681
r_angle_refined_deg1.939
r_mcangle_it1.797
r_mcbond_it1.222
r_nbtor_refined0.32
r_symmetry_vdw_refined0.234
r_nbd_refined0.228
r_symmetry_hbond_refined0.218
r_xyhbond_nbd_refined0.168
r_chiral_restr0.137
r_metal_ion_refined0.057
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5486
Nucleic Acid Atoms
Solvent Atoms874
Heterogen Atoms193

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling