4OME

X-ray structure of human glutamate carboxypeptidase II in complex with DCCBL, a urea based inhibitor with distal carborane moiety


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829333% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5 % (w/v) PEG 3350, 100 mM Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.2862.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.316α = 90
b = 130.564β = 90
c = 158.073γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-04-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.11.0BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.795099.39722097220-3-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.791.996

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT1.7928.439233792336485999.330.158750.157440.18404RANDOM25.962
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]
-0.150.4-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.609
r_dihedral_angle_4_deg14.869
r_dihedral_angle_3_deg13.307
r_dihedral_angle_1_deg5.991
r_scbond_it1.982
r_mcangle_it1.796
r_angle_refined_deg1.576
r_mcbond_it1.152
r_chiral_restr0.114
r_bond_refined_d0.015
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.609
r_dihedral_angle_4_deg14.869
r_dihedral_angle_3_deg13.307
r_dihedral_angle_1_deg5.991
r_scbond_it1.982
r_mcangle_it1.796
r_angle_refined_deg1.576
r_mcbond_it1.152
r_chiral_restr0.114
r_bond_refined_d0.015
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_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms5512
Nucleic Acid Atoms
Solvent Atoms574
Heterogen Atoms227

Software

Software
Software NamePurpose
MAR345dtbdata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing