3IWW

Crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DBIBzL, a urea-based inhibitor


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% v/v pentaerythritol propoxylate PO/OH 5/4, 1.5 % w/v PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2562.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.068α = 90
b = 130.035β = 90
c = 157.951γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDhigh-resolution Rosenbaum-Rock monochromator for sagital focusing, Rosenbaum-Rock vertical focusing mirror2008-12-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-ID1.0000APS22-ID

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
12.152099.80.125165.65642756427-3
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)
12.152.2398.50.4473.23.95526

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2OOT2.32044049142097.930.166210.164890.20581RANDOM23.613
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]
2.46-3.220.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.871
r_dihedral_angle_3_deg16.62
r_dihedral_angle_4_deg16.437
r_dihedral_angle_1_deg6.233
r_scangle_it5.079
r_scbond_it3.097
r_angle_refined_deg1.822
r_mcangle_it1.735
r_mcbond_it0.927
r_chiral_restr0.122
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.871
r_dihedral_angle_3_deg16.62
r_dihedral_angle_4_deg16.437
r_dihedral_angle_1_deg6.233
r_scangle_it5.079
r_scbond_it3.097
r_angle_refined_deg1.822
r_mcangle_it1.735
r_mcbond_it0.927
r_chiral_restr0.122
r_bond_refined_d0.02
r_gen_planes_refined0.009
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
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5529
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms209

Software

Software
Software NamePurpose
MAR345data collection
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
REFMACphasing