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1.55 A resolution 3,6-dimethylcatechol (3,6-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 2.76 55.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.463 α = 90 b = 131.463 β = 90 c = 189.067 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 0.9677 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 1.55 48.77 99.9 0.127 0.135 0.046 0.999 17.8 16 139215 13.2
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 1.55 1.58 97.5 2.145 2.288 0.792 0.67 1.5 15.6
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 1.55 47.311 139006 6983 99.967 0.136 0.1355 0.1485 0.156 0.1656 20.213
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] 0.681 0.34 0.681 -2.209
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.199 r_dihedral_angle_4_deg 18.057 r_dihedral_angle_3_deg 12.389 r_dihedral_angle_1_deg 7.01 r_lrange_it 5.592 r_lrange_other 5.592 r_scangle_it 4.037 r_scangle_other 3.827 r_scbond_it 2.723 r_scbond_other 2.581
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.199 r_dihedral_angle_4_deg 18.057 r_dihedral_angle_3_deg 12.389 r_dihedral_angle_1_deg 7.01 r_lrange_it 5.592 r_lrange_other 5.592 r_scangle_it 4.037 r_scangle_other 3.827 r_scbond_it 2.723 r_scbond_other 2.581 r_mcangle_it 1.943 r_mcangle_other 1.943 r_angle_refined_deg 1.765 r_angle_other_deg 1.507 r_mcbond_it 1.408 r_mcbond_other 1.408 r_symmetry_nbd_refined 0.226 r_nbd_refined 0.223 r_nbd_other 0.207 r_symmetry_nbd_other 0.189 r_nbtor_refined 0.164 r_xyhbond_nbd_refined 0.155 r_symmetry_xyhbond_nbd_refined 0.154 r_symmetry_xyhbond_nbd_other 0.105 r_symmetry_nbtor_other 0.097 r_chiral_restr 0.093 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 6034 Nucleic Acid Atoms Solvent Atoms 758 Heterogen Atoms 136
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing