3BI0

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of Glu-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
3.3463.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.405α = 90
b = 130.797β = 90
c = 159.14γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2006-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.000APS22-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
11.675097.40.09123.410.9119268119268-3-3
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)
11.671.7379.10.522.16.19667

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 2oot1.6715117320178696.930.183770.183370.21142RANDOM28.817
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]
0.9-1.780.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_4_deg15.924
r_dihedral_angle_3_deg14.438
r_sphericity_free8.68
r_sphericity_bonded8.602
r_dihedral_angle_1_deg5.921
r_scangle_it4.279
r_scbond_it2.733
r_mcangle_it1.784
r_angle_refined_deg1.783
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.437
r_dihedral_angle_4_deg15.924
r_dihedral_angle_3_deg14.438
r_sphericity_free8.68
r_sphericity_bonded8.602
r_dihedral_angle_1_deg5.921
r_scangle_it4.279
r_scbond_it2.733
r_mcangle_it1.784
r_angle_refined_deg1.783
r_mcbond_it1.098
r_chiral_restr0.13
r_bond_refined_d0.021
r_gen_planes_refined0.01
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 Atoms644
Heterogen Atoms200

Software

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