☰ Navigation Tabs
Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 6.3 293 Protein-ligand (1 mM ligand concentration) complex in 50 mM HEPES buffer, pH 7.50 (also containing 10% (V/V) DMSO), diluted 1:1 with 1.6-2.1 M ammonium sulfate also containing 100 mM sodium citrate at pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.72 54.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.612 α = 90 b = 131.612 β = 90 c = 189.003 γ = 120
Symmetry Space Group P 63 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 2020-10-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9763 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) 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 1.54 189 100 0.094 0.099 0.031 1 20.9 19.5 142031 21.21
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 1.54 1.57 100 2.301 2.422 0.752 0.749 1.6 19.9
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5G4H 1.54 97.8 134952 7016 99.95 0.13857 0.13747 0.15991 0.1508 RANDOM 25.426
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] 0.7 0.35 0.7 -2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_4_deg 19.263 r_dihedral_angle_3_deg 12.928 r_dihedral_angle_1_deg 7.093 r_long_range_B_other 5.923 r_long_range_B_refined 5.922 r_scangle_other 4.506 r_scbond_it 3.237 r_scbond_other 3.234 r_mcangle_it 2.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.735 r_dihedral_angle_4_deg 19.263 r_dihedral_angle_3_deg 12.928 r_dihedral_angle_1_deg 7.093 r_long_range_B_other 5.923 r_long_range_B_refined 5.922 r_scangle_other 4.506 r_scbond_it 3.237 r_scbond_other 3.234 r_mcangle_it 2.53 r_mcangle_other 2.53 r_mcbond_it 1.844 r_mcbond_other 1.842 r_angle_refined_deg 1.806 r_angle_other_deg 1.5 r_chiral_restr 0.099 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 767 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing