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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a urea based inhibitor PSMA 1023
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI1 3BI1.pdb
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293.15 34 % (v/v) pentaerythritol propoxylate PO/OH 5/4,
2 % (w/v) PEG 3350,
100 mM Tris-HCl, pH 8.0.
Crystal Properties Matthews coefficient Solvent content 3.3 62.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.512 α = 90 b = 130.203 β = 90 c = 159.16 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-01-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.918 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.65 49.13 99.1 0.055 0.029 0.999 15.4 4.5 125247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 96.4 0.953 0.493 0.762 1.7 4.6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3BI1.pdb 1.65 49.13 118929 6313 99 0.1262 0.12442 0.15989 0.1622 RANDOM 36.995
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] 0.33 -1.63 1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_sphericity_free 23.551 r_dihedral_angle_4_deg 15.837 r_dihedral_angle_3_deg 13.609 r_sphericity_bonded 12.516 r_dihedral_angle_1_deg 5.903 r_rigid_bond_restr 5.597 r_long_range_B_refined 3.827 r_scangle_other 3.812 r_long_range_B_other 3.645
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.668 r_sphericity_free 23.551 r_dihedral_angle_4_deg 15.837 r_dihedral_angle_3_deg 13.609 r_sphericity_bonded 12.516 r_dihedral_angle_1_deg 5.903 r_rigid_bond_restr 5.597 r_long_range_B_refined 3.827 r_scangle_other 3.812 r_long_range_B_other 3.645 r_scbond_it 3.416 r_scbond_other 3.415 r_mcangle_it 2.742 r_mcangle_other 2.742 r_mcbond_it 2.405 r_mcbond_other 2.335 r_angle_other_deg 2.09 r_angle_refined_deg 1.563 r_chiral_restr 0.099 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.008 r_bond_other_d 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5546 Nucleic Acid Atoms Solvent Atoms 624 Heterogen Atoms 304
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling Coot model building