☰ Navigation Tabs
1.47A human IMPase with ebselen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6GJ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 0.2M MnS04, 0.1M MES, 28% PEG4000 and pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.52 51.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.02 α = 90 b = 84.02 β = 90 c = 150.22 γ = 120
Symmetry Space Group P 32 2 1
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-F 2019-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91188 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim 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 1.47 24.44 100 0.053 0.022 1 20.4 11 104886
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.47 1.5 2.019 2.123 0.652 0.498 1.2
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS FREE R-VALUE 6gj0 1.47 24.438 104821 5081 99.966 0.181 0.1791 0.1791 0.2083 0.2083 30.088
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] -0.032 -0.016 -0.032 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.5 r_dihedral_angle_4_deg 14.469 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 8.411 r_lrange_it 6.854 r_scangle_it 5.276 r_scbond_it 3.84 r_mcangle_it 3.536 r_mcbond_it 2.567 r_angle_refined_deg 1.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.5 r_dihedral_angle_4_deg 14.469 r_dihedral_angle_3_deg 13.783 r_dihedral_angle_1_deg 8.411 r_lrange_it 6.854 r_scangle_it 5.276 r_scbond_it 3.84 r_mcangle_it 3.536 r_mcbond_it 2.567 r_angle_refined_deg 1.901 r_metal_ion_refined 0.359 r_nbtor_refined 0.323 r_xyhbond_nbd_refined 0.276 r_nbd_refined 0.241 r_symmetry_nbd_refined 0.239 r_symmetry_xyhbond_nbd_refined 0.235 r_chiral_restr 0.14 r_symmetry_metal_ion_refined 0.109 r_bond_refined_d 0.011 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4106 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 122
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing