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1.28 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3UBP
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 2.76 55.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.742 α = 90 b = 131.742 β = 90 c = 188.93 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 2016-06-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.934 PETRA III, EMBL c/o DESY P13 (MX1)
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 1.28 114.09 99.4 0.117 0.033 0.999 15.9 14.3 243939 10.4
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 1.28 1.3 98.1 2.2 0.625 0.673 1.5 14.6
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 3UBP 1.28 114.09 231654 12246 99.26 0.11992 0.11903 0.119 0.13684 0.1363 RANDOM 14.901
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] 0.23 0.12 0.23 -0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.359 r_sphericity_free 26.481 r_dihedral_angle_4_deg 17.406 r_dihedral_angle_3_deg 11.775 r_rigid_bond_restr 8.153 r_sphericity_bonded 6.804 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 2.567 r_long_range_B_other 2.567 r_scangle_other 1.935
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.359 r_sphericity_free 26.481 r_dihedral_angle_4_deg 17.406 r_dihedral_angle_3_deg 11.775 r_rigid_bond_restr 8.153 r_sphericity_bonded 6.804 r_dihedral_angle_1_deg 6.149 r_long_range_B_refined 2.567 r_long_range_B_other 2.567 r_scangle_other 1.935 r_scbond_it 1.547 r_scbond_other 1.547 r_angle_refined_deg 1.377 r_mcangle_it 0.928 r_mcangle_other 0.928 r_angle_other_deg 0.808 r_mcbond_it 0.685 r_mcbond_other 0.685 r_chiral_restr 0.085 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 782 Heterogen Atoms 90
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing