4W9Y

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a glutamyl sulfamide inhibitor CJC47


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP828834% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5 % (w/v) PEG 3350, and 100 mM Tris-HCl, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
3.2862.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.189α = 90
b = 130.425β = 90
c = 158.452γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252013-02-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.918BESSY14.2

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
11.645099.20.066195.894692
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.641.7395.72.55.8

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.6428.4312136863881000.159510.158590.17694RANDOM26.886
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.981
r_dihedral_angle_4_deg16.036
r_dihedral_angle_3_deg13.651
r_dihedral_angle_1_deg5.915
r_scangle_it4.202
r_scbond_it2.59
r_angle_refined_deg1.63
r_mcangle_it1.535
r_mcbond_it0.895
r_chiral_restr0.124
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.981
r_dihedral_angle_4_deg16.036
r_dihedral_angle_3_deg13.651
r_dihedral_angle_1_deg5.915
r_scangle_it4.202
r_scbond_it2.59
r_angle_refined_deg1.63
r_mcangle_it1.535
r_mcbond_it0.895
r_chiral_restr0.124
r_bond_refined_d0.018
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5495
Nucleic Acid Atoms
Solvent Atoms582
Heterogen Atoms194

Software

Software
Software NamePurpose
REFMACrefinement