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The 1.68-A X-ray crystal structure of Sporosarcina pasteurii urease inhibited by thiram and bound to dimethylditiocarbamate
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 6.5 293 100 mM citrate, pH 6.3, 1.6-2.1 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.72 54.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.511 α = 90 b = 131.511 β = 90 c = 189.017 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 2018-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.97 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 1.68 114.5 100 0.136 0.142 0.032 0.999 18.9 19.7 109674
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 1.68 1.71 100 2.4 2.5 0.556 0.738 1.6 20.4
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 1.68 114.15 104151 5465 99.93 0.13942 0.13815 0.1531 0.16318 0.1737 RANDOM 26.285
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] 1.04 0.52 1.04 -3.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.967 r_dihedral_angle_2_deg 8.377 r_long_range_B_refined 8.273 r_long_range_B_other 8.273 r_dihedral_angle_1_deg 6.906 r_scangle_other 4.952 r_scbond_it 3.933 r_scbond_other 3.441 r_mcangle_it 2.667 r_mcangle_other 2.667
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.967 r_dihedral_angle_2_deg 8.377 r_long_range_B_refined 8.273 r_long_range_B_other 8.273 r_dihedral_angle_1_deg 6.906 r_scangle_other 4.952 r_scbond_it 3.933 r_scbond_other 3.441 r_mcangle_it 2.667 r_mcangle_other 2.667 r_mcbond_it 2.042 r_mcbond_other 2.04 r_angle_refined_deg 1.698 r_angle_other_deg 0.571 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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 6058 Nucleic Acid Atoms Solvent Atoms 554 Heterogen Atoms 162
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing