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X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with an inhibitor Ac-gamma-Glu-Dap(thiooxalyl)-OH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BI1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 32% (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 3.33 63.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.672 α = 90 b = 130.61 β = 90 c = 159.503 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 PILATUS3 6M 2015-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 1.033 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.54 50 99.6 0.046 0.999 16.01 4.82 155895
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.54 1.63 98.8 0.591 0.863 1.91 4.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 1.54 49.24 1.35 155758 2097 99.52 0.1727 0.1724 0.1726 0.1909 0.1917
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 Key Refinement Restraint Deviation f_dihedral_angle_d 16.6 f_angle_d 1.212 f_chiral_restr 0.076 f_bond_d 0.012 f_plane_restr 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5545 Nucleic Acid Atoms Solvent Atoms 593 Heterogen Atoms 280
Software Software Software Name Purpose PHENIX refinement REFMAC phasing XDS data reduction Aimless data scaling