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X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a inhibitor sulfamide inhibitor GluAsp
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 33% (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 3.36 63.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.629 α = 90 b = 130.53 β = 90 c = 159.192 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 2015-10-31 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) 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 99.2 0.033 0.042 0.999 19.5 4.4 143110
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 1.61 97.8 0.528 0.678 0.86 2.5 4.3
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 49.21 136083 7026 99.12 0.1722 0.1712 0.1777 0.1928 0.2046 RANDOM 29.211
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] 1.33 -2.03 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.963 r_dihedral_angle_4_deg 15.85 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 6.188 r_angle_other_deg 4.211 r_mcangle_it 2.267 r_mcbond_it 1.515 r_mcbond_other 1.515 r_angle_refined_deg 1.277 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.963 r_dihedral_angle_4_deg 15.85 r_dihedral_angle_3_deg 13.23 r_dihedral_angle_1_deg 6.188 r_angle_other_deg 4.211 r_mcangle_it 2.267 r_mcbond_it 1.515 r_mcbond_other 1.515 r_angle_refined_deg 1.277 r_chiral_restr 0.083 r_gen_planes_other 0.011 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5545 Nucleic Acid Atoms Solvent Atoms 591 Heterogen Atoms 300
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing Coot model building