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1.49 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 6.5
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 6.5 293 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 6.5.
Crystal Properties Matthews coefficient Solvent content 2.75 55.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.813 α = 90 b = 131.813 β = 90 c = 189.028 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) 0.9797 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 1.49 114.15 99.8 0.123 0.133 0.036 0.999 15.3 13.2 156618 13.3
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 1.49 1.52 99.4 1.933 2.115 0.607 0.575 1.5 11.8
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 5OL4 1.49 114.15 148730 7859 99.74 0.13702 0.13619 0.1359 0.15302 0.1528 RANDOM 19.406
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] 0.54 0.27 0.54 -1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.392 r_dihedral_angle_4_deg 17.889 r_dihedral_angle_3_deg 11.749 r_dihedral_angle_1_deg 6.047 r_long_range_B_refined 5.307 r_long_range_B_other 5.306 r_scangle_other 2.941 r_scbond_it 1.878 r_scbond_other 1.878 r_mcangle_it 1.532
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.392 r_dihedral_angle_4_deg 17.889 r_dihedral_angle_3_deg 11.749 r_dihedral_angle_1_deg 6.047 r_long_range_B_refined 5.307 r_long_range_B_other 5.306 r_scangle_other 2.941 r_scbond_it 1.878 r_scbond_other 1.878 r_mcangle_it 1.532 r_mcangle_other 1.532 r_angle_refined_deg 1.442 r_mcbond_it 0.991 r_mcbond_other 0.989 r_angle_other_deg 0.8 r_chiral_restr 0.088 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6046 Nucleic Acid Atoms Solvent Atoms 709 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing