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1.32 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5OL4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 Protein dissolved in 50 mM HEPES, pH 7.5, 2 mM EDTA, 4 mM NBPTO. Precipitant solution consisting of 100 mM citrate buffer, 1.7-1.9 M ammonium sulfate, 4 mM NBPTO, at pH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.76 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.783 α = 90 b = 131.783 β = 90 c = 188.768 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 2018-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.979700 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 1.32 97.67 98.8 0.118 0.128 0.035 0.999 13.3 13.2 221217
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 1.32 1.34 97.4 2.23 2.392 0.633 0.653 1.5 13.8
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5OL4 1.32 97.67 210078 11101 98.64 0.12275 0.1217 0.14254 0.1427 RANDOM 16.396
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] -0.14 -0.07 -0.14 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.389 r_sphericity_free 32.819 r_dihedral_angle_4_deg 16.659 r_sphericity_bonded 12.692 r_dihedral_angle_3_deg 11.708 r_scangle_other 6.581 r_dihedral_angle_1_deg 6.244 r_scbond_it 5.174 r_scbond_other 5.157 r_long_range_B_refined 4.635
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.389 r_sphericity_free 32.819 r_dihedral_angle_4_deg 16.659 r_sphericity_bonded 12.692 r_dihedral_angle_3_deg 11.708 r_scangle_other 6.581 r_dihedral_angle_1_deg 6.244 r_scbond_it 5.174 r_scbond_other 5.157 r_long_range_B_refined 4.635 r_long_range_B_other 4.634 r_rigid_bond_restr 2.304 r_mcangle_it 1.941 r_mcangle_other 1.941 r_mcbond_other 1.557 r_mcbond_it 1.556 r_angle_refined_deg 1.345 r_angle_other_deg 0.795 r_chiral_restr 0.082 r_bond_refined_d 0.007 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 741 Heterogen Atoms 109
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing