☰ Navigation Tabs
X-ray structure of human glutamate carboxypeptidase II (GCPII)-E424M inactive mutant, in complex with a inhibitor KB1160
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 32% (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 62.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.404 α = 90 b = 130.15 β = 90 c = 159.268 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 2M 2019-01-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.918 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.76 50 99.6 0.072 15.91 6 104162
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.76 1.86 0.823
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.76 45 102046 2099 99.66 0.16771 0.16716 0.1715 0.19404 0.1964 RANDOM 37.289
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] 0.01 -0.04 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.341 r_dihedral_angle_4_deg 15.227 r_dihedral_angle_3_deg 14.548 r_dihedral_angle_1_deg 6.517 r_long_range_B_refined 5.918 r_scbond_it 2.72 r_mcangle_it 2.414 r_mcbond_it 1.786 r_angle_refined_deg 1.741 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.341 r_dihedral_angle_4_deg 15.227 r_dihedral_angle_3_deg 14.548 r_dihedral_angle_1_deg 6.517 r_long_range_B_refined 5.918 r_scbond_it 2.72 r_mcangle_it 2.414 r_mcbond_it 1.786 r_angle_refined_deg 1.741 r_chiral_restr 0.119 r_bond_refined_d 0.011 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 5545 Nucleic Acid Atoms Solvent Atoms 572 Heterogen Atoms 236
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing