3BHX

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of Asp-Glu


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, 1% (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.362.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.554α = 90
b = 130.258β = 90
c = 159.192γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-11-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM0.976APS22-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
11.63097.90.04220.73.9135043135043-3-3
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)
11.61.6695.60.294.33.913157

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 2oot1.615134043163997.950.180790.180540.20154RANDOM26.329
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]
1.16-2.050.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.431
r_dihedral_angle_4_deg15.946
r_dihedral_angle_3_deg14.407
r_sphericity_bonded10.898
r_sphericity_free6.733
r_dihedral_angle_1_deg5.887
r_scangle_it4.269
r_scbond_it2.735
r_angle_refined_deg1.878
r_mcangle_it1.817
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.431
r_dihedral_angle_4_deg15.946
r_dihedral_angle_3_deg14.407
r_sphericity_bonded10.898
r_sphericity_free6.733
r_dihedral_angle_1_deg5.887
r_scangle_it4.269
r_scbond_it2.735
r_angle_refined_deg1.878
r_mcangle_it1.817
r_mcbond_it1.116
r_chiral_restr0.133
r_bond_refined_d0.02
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5529
Nucleic Acid Atoms
Solvent Atoms665
Heterogen Atoms198

Software

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