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X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with an inhibitor 617
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI1 3BI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 33% (v/v) pentaerythritol propoxylate PO/OH 5/4
1 % (w/v) PEG 3350
100 mM Tris-HCl, pH 8.0
Crystal Properties Matthews coefficient Solvent content 3.3 62.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.281 α = 90 b = 130 β = 90 c = 159.492 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 90 PIXEL DECTRIS PILATUS 6M 2015-08-29 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) Rrim 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 1.58 50 99.5 0.055 0.061 0.999 17.86 5.2 143725
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.58 1.67 97.9 0.71 0.793 0.805 1.98 4.98
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3BI1 1.58 45.25 141700 2100 99.59 0.18082 0.18056 0.1803 0.19789 0.1976 RANDOM 26.284
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] 1.01 -1.93 0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.651 r_dihedral_angle_4_deg 14.286 r_dihedral_angle_3_deg 13.373 r_dihedral_angle_1_deg 5.871 r_long_range_B_refined 5.43 r_scbond_it 2.199 r_mcangle_it 1.875 r_angle_refined_deg 1.508 r_mcbond_it 1.292 r_chiral_restr 0.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.651 r_dihedral_angle_4_deg 14.286 r_dihedral_angle_3_deg 13.373 r_dihedral_angle_1_deg 5.871 r_long_range_B_refined 5.43 r_scbond_it 2.199 r_mcangle_it 1.875 r_angle_refined_deg 1.508 r_mcbond_it 1.292 r_chiral_restr 0.097 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5514 Nucleic Acid Atoms Solvent Atoms 635 Heterogen Atoms 322
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing