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X-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a inhibitor JHU 2249
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 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 3.34 63.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.702 α = 90 b = 130.687 β = 90 c = 159.829 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 2016-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9796 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 1.52 30 99.4 0.048 0.053 0.999 15.89 5.09 161939 -3 -3
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 1.52 1.62 97.3 0.551 0.619 0.898 2.23 4.83
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3BI1.pdb 1.52 30 -3 156947 4964 99.52 0.15866 0.15803 0.1615 0.179 0.1815 RANDOM 32.437
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] 1.11 -2.08 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.896 r_dihedral_angle_4_deg 14.517 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 6.083 r_long_range_B_refined 5.663 r_scbond_it 2.257 r_mcangle_it 1.965 r_angle_refined_deg 1.793 r_mcbond_it 1.312 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.896 r_dihedral_angle_4_deg 14.517 r_dihedral_angle_3_deg 13.607 r_dihedral_angle_1_deg 6.083 r_long_range_B_refined 5.663 r_scbond_it 2.257 r_mcangle_it 1.965 r_angle_refined_deg 1.793 r_mcbond_it 1.312 r_chiral_restr 0.129 r_bond_refined_d 0.018 r_gen_planes_refined 0.011 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 5515 Nucleic Acid Atoms Solvent Atoms 579 Heterogen Atoms 234
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing Coot model building