☰ Navigation Tabs
1.50 A resolution 3-methylcatechol (3-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 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.577 α = 90 b = 131.577 β = 90 c = 189.365 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 2016-07-13 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 1.5 113.949 99.7 0.113 0.121 0.042 0.999 18.8 15.4 153039 15.9
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 1.5 1.53 99.1 2.359 2.526 0.9 0.687 1.5 14.9
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5G4H 1.5 94.862 153002 7683 99.572 0.134 0.133 0.1521 0.1378 21.148
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] 0.742 0.371 0.742 -2.406
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.393 r_dihedral_angle_4_deg 18.228 r_dihedral_angle_3_deg 12.308 r_dihedral_angle_1_deg 6.959 r_lrange_it 5.443 r_lrange_other 5.259 r_scangle_it 4.315 r_scangle_other 4.174 r_scbond_it 2.961 r_scbond_other 2.846
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.393 r_dihedral_angle_4_deg 18.228 r_dihedral_angle_3_deg 12.308 r_dihedral_angle_1_deg 6.959 r_lrange_it 5.443 r_lrange_other 5.259 r_scangle_it 4.315 r_scangle_other 4.174 r_scbond_it 2.961 r_scbond_other 2.846 r_mcangle_other 2.071 r_mcangle_it 2.07 r_angle_refined_deg 1.755 r_angle_other_deg 1.491 r_mcbond_it 1.462 r_mcbond_other 1.46 r_nbd_refined 0.213 r_symmetry_nbd_refined 0.2 r_nbd_other 0.187 r_symmetry_nbd_other 0.176 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.158 r_symmetry_xyhbond_nbd_refined 0.158 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.081 r_symmetry_xyhbond_nbd_other 0.074 r_bond_refined_d 0.011 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 6041 Nucleic Acid Atoms Solvent Atoms 716 Heterogen Atoms 169
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing