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2.23 A resolution 3,4-dimethylcatechol (3,4-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 2.75 55.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.501 α = 90 b = 131.501 β = 90 c = 188.71 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 2020-02-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.000 ELETTRA 11.2C
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 2.23 188.71 100 0.271 0.299 0.125 0.995 9 10.7 47585 27.9
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 2.23 2.3 100 1.751 1.929 0.804 0.657 1.5 11
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 2.23 113.883 47536 2279 99.971 0.164 0.1611 0.1611 0.2162 0.2158 34.357
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] 1.038 0.519 1.038 -3.368
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.16 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 16.035 r_lrange_it 9.216 r_dihedral_angle_1_deg 7.57 r_scangle_it 6.299 r_scbond_it 4.562 r_mcangle_it 3.808 r_mcbond_it 2.757 r_angle_refined_deg 1.861
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.16 r_dihedral_angle_4_deg 19.595 r_dihedral_angle_3_deg 16.035 r_lrange_it 9.216 r_dihedral_angle_1_deg 7.57 r_scangle_it 6.299 r_scbond_it 4.562 r_mcangle_it 3.808 r_mcbond_it 2.757 r_angle_refined_deg 1.861 r_nbtor_refined 0.317 r_nbd_refined 0.227 r_symmetry_nbd_refined 0.198 r_symmetry_xyhbond_nbd_refined 0.186 r_xyhbond_nbd_refined 0.178 r_chiral_restr 0.122 r_bond_refined_d 0.009 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6041 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 152
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing