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Sporosarcina pasteurii urease in complex with an Ebsulfur derivative at 1.95 A
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 VAPOR DIFFUSION, HANGING DROP 6.3 293 1.6-2.1 M ammonium sulfate, 100 mM citrate, pH 6.3
Crystal Properties Matthews coefficient Solvent content 2.74 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.368 α = 90 b = 131.368 β = 90 c = 188.863 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 2024-05-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.976 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 1.95 48.73 99.9 0.195 0.21 0.057 0.998 10.3 13.6 70426 24.53
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 1.95 1.99 100 1.955 2.102 0.567 0.79 1.6
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 MOLECULAR REPLACEMENT THROUGHOUT 1.95 48.73 66851 3532 99.88 0.15091 0.14896 0.1498 0.18688 0.1879 RANDOM 31.725
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] 1.09 0.55 1.09 -3.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.847 r_dihedral_angle_2_deg 7.705 r_long_range_B_refined 7.534 r_dihedral_angle_1_deg 7.093 r_scbond_it 4.199 r_mcangle_it 3.097 r_mcbond_it 2.391 r_angle_refined_deg 1.642 r_chiral_restr 0.108 r_bond_refined_d 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.847 r_dihedral_angle_2_deg 7.705 r_long_range_B_refined 7.534 r_dihedral_angle_1_deg 7.093 r_scbond_it 4.199 r_mcangle_it 3.097 r_mcbond_it 2.391 r_angle_refined_deg 1.642 r_chiral_restr 0.108 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_4_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 6047 Nucleic Acid Atoms Solvent Atoms 452 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing