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1.61 A resolution 3,5-dimethylcatechol (3,5-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 2.76 55.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.566 α = 90 b = 131.566 β = 90 c = 188.919 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 2017-07-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.966 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 1.61 45.49 99.8 0.097 0.109 0.05 0.999 12.4 8.7 123908 21.3
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 1.61 1.64 99.6 1.659 1.867 0.845 0.61 1.5 8.9
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 (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 1.61 45.49 123886 6228 99.637 0.137 0.1357 0.1499 0.159 0.1695 24.4
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] 0.786 0.393 0.786 -2.549
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.941 r_dihedral_angle_4_deg 18.715 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_1_deg 6.976 r_lrange_it 6.664 r_lrange_other 6.664 r_scangle_it 5.241 r_scangle_other 4.719 r_scbond_it 3.777 r_scbond_other 3.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.941 r_dihedral_angle_4_deg 18.715 r_dihedral_angle_3_deg 12.753 r_dihedral_angle_1_deg 6.976 r_lrange_it 6.664 r_lrange_other 6.664 r_scangle_it 5.241 r_scangle_other 4.719 r_scbond_it 3.777 r_scbond_other 3.268 r_mcangle_it 2.419 r_mcangle_other 2.419 r_angle_refined_deg 1.822 r_mcbond_it 1.765 r_mcbond_other 1.765 r_angle_other_deg 1.499 r_symmetry_nbd_refined 0.257 r_nbd_refined 0.213 r_nbd_other 0.21 r_symmetry_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.17 r_nbtor_refined 0.165 r_chiral_restr 0.098 r_symmetry_xyhbond_nbd_other 0.087 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 567 Heterogen Atoms 210
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing