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1.45 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPTO
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 6.3 293 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 2.75 55.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.446 α = 90 b = 131.446 β = 90 c = 188.716 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 EIGER X 4M 2018-03-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.967700 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.45 48.74 99.1 0.107 0.031 0.999 16.2 13.8 168094
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.47 97.9 1.94 0.578 0.655 1.5 12.8
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 1.45 48.74 159601 8446 99.47 0.1253 0.12434 0.1246 0.14316 0.1432 RANDOM 18.867
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] 0.57 0.29 0.57 -1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_sphericity_free 20.347 r_dihedral_angle_4_deg 18.271 r_dihedral_angle_3_deg 12.283 r_dihedral_angle_1_deg 6.119 r_sphericity_bonded 4.982 r_long_range_B_refined 2.322 r_long_range_B_other 2.305 r_scangle_other 2.247 r_rigid_bond_restr 2.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_sphericity_free 20.347 r_dihedral_angle_4_deg 18.271 r_dihedral_angle_3_deg 12.283 r_dihedral_angle_1_deg 6.119 r_sphericity_bonded 4.982 r_long_range_B_refined 2.322 r_long_range_B_other 2.305 r_scangle_other 2.247 r_rigid_bond_restr 2.195 r_scbond_it 1.902 r_scbond_other 1.901 r_angle_refined_deg 1.356 r_mcangle_it 1.294 r_mcangle_other 1.294 r_mcbond_it 1.081 r_mcbond_other 1.081 r_angle_other_deg 0.787 r_chiral_restr 0.08 r_bond_refined_d 0.007 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6047 Nucleic Acid Atoms Solvent Atoms 626 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing