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1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporosarcina pasteurii urease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AC7 PDB ENTRY 4AC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 1.8 M AMMONIUM SULFATE, 50 MM SODIUM CITRATE BUFFER, PH 6.3
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.276 α = 90 b = 131.276 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 2015-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.5 94.51 100 0.07 23.1 11.8 152722 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.53 99.9 1.31 1.6 9.8
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 (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 PDB ENTRY 4AC7 1.5 113.69 144972 7662 99.96 0.12285 0.12118 0.1388 0.15423 0.168 RANDOM 23.351
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] 1.05 0.53 1.05 -3.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_sphericity_free 34.259 r_dihedral_angle_4_deg 16.573 r_sphericity_bonded 11.931 r_dihedral_angle_3_deg 11.67 r_dihedral_angle_1_deg 6.16 r_scbond_it 3.402 r_mcangle_it 2.248 r_rigid_bond_restr 2.15 r_mcbond_it 1.958
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.653 r_sphericity_free 34.259 r_dihedral_angle_4_deg 16.573 r_sphericity_bonded 11.931 r_dihedral_angle_3_deg 11.67 r_dihedral_angle_1_deg 6.16 r_scbond_it 3.402 r_mcangle_it 2.248 r_rigid_bond_restr 2.15 r_mcbond_it 1.958 r_mcbond_other 1.957 r_angle_refined_deg 1.369 r_angle_other_deg 0.778 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6044 Nucleic Acid Atoms Solvent Atoms 675 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling CCP4 phasing