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1.89 A resolution 4-methylcatechol (4-methylbenzene-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 2.74 55.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.021 α = 90 b = 131.021 β = 90 c = 188.879 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 2015-06-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9537 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 1.89 97.27 99.8 0.124 0.159 0.098 0.994 9.5 4.4 76691 17.2
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 1.89 1.93 99.8 0.842 1.099 0.698 0.675 1.5 4.1
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 1.89 97.27 76656 3779 99.709 0.16 0.1591 0.159 0.1781 0.1784 27.624
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] 1.181 0.591 1.181 -3.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 13.708 r_dihedral_angle_1_deg 7.236 r_lrange_it 6.548 r_scangle_it 4.853 r_scbond_it 3.534 r_mcangle_it 2.594 r_mcbond_it 1.943 r_angle_refined_deg 1.653
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.681 r_dihedral_angle_4_deg 18.688 r_dihedral_angle_3_deg 13.708 r_dihedral_angle_1_deg 7.236 r_lrange_it 6.548 r_scangle_it 4.853 r_scbond_it 3.534 r_mcangle_it 2.594 r_mcbond_it 1.943 r_angle_refined_deg 1.653 r_nbtor_refined 0.306 r_nbd_refined 0.214 r_symmetry_nbd_refined 0.197 r_symmetry_xyhbond_nbd_refined 0.163 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.105 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6040 Nucleic Acid Atoms Solvent Atoms 584 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing