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1.65 A resolution 4,5-dimethylcatechol (4,5-dimethylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease
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 50 mM citrate buffer at pH 6.3, containing 1.6 - 2.0 M ammonium sulfate as a precipitant
Crystal Properties Matthews coefficient Solvent content 2.77 55.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.64 α = 90 b = 131.64 β = 90 c = 189.254 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 EIGER X 4M 2018-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.96769 ESRF ID30B
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 1.65 62.245 100 0.131 0.137 0.042 0.999 18.6 20.5 116041 20.6
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 1.65 1.68 100 2.811 2.947 0.883 0.771 1.5 21.2
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 MOLECULAR REPLACEMENT FREE R-VALUE 5G4H 1.65 62.24 115979 5813 99.974 0.136 0.1344 0.1491 0.1556 0.1677 24.979
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] 0.729 0.365 0.729 -2.366
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.325 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 12.236 r_dihedral_angle_1_deg 7.018 r_lrange_it 6.338 r_lrange_other 6.338 r_scangle_it 4.819 r_scangle_other 4.403 r_scbond_it 3.261 r_scbond_other 3.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.325 r_dihedral_angle_4_deg 17.885 r_dihedral_angle_3_deg 12.236 r_dihedral_angle_1_deg 7.018 r_lrange_it 6.338 r_lrange_other 6.338 r_scangle_it 4.819 r_scangle_other 4.403 r_scbond_it 3.261 r_scbond_other 3.015 r_mcangle_it 2.278 r_mcangle_other 2.278 r_angle_refined_deg 1.745 r_mcbond_it 1.666 r_mcbond_other 1.664 r_angle_other_deg 1.475 r_symmetry_nbd_refined 0.218 r_nbd_refined 0.211 r_nbd_other 0.206 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.162 r_symmetry_xyhbond_nbd_refined 0.158 r_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.137 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6041 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 170
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing