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1.75 A resolution 2,5-dihydroxybenzensulfonate inhibited Sporosarcina pasteurii urease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4AC7 PDB ENTRY 4AC7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 1.8 M AMMONIUM SULFATE, 50 MM SODIUM CITRATE BUFFER PH 6.3, 50 MM SODIUM SULFITE
Crystal Properties Matthews coefficient Solvent content 2.75 55.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.312 α = 90 b = 131.312 β = 90 c = 188.92 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 2015-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 97.43 100 0.1 20 12.8 96874 1.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 100 1.45 1.6 11
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 PDB ENTRY 4AC7 1.75 113.72 92058 4763 99.98 0.13592 0.13418 0.1489 0.16973 0.1795 RANDOM 28.466
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] 0.93 0.46 0.93 -3.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.953 r_dihedral_angle_4_deg 17.079 r_dihedral_angle_3_deg 12.746 r_dihedral_angle_1_deg 6.454 r_scbond_it 3.541 r_mcangle_it 2.739 r_mcbond_it 2.123 r_mcbond_other 2.119 r_angle_refined_deg 1.97 r_angle_other_deg 0.912
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.953 r_dihedral_angle_4_deg 17.079 r_dihedral_angle_3_deg 12.746 r_dihedral_angle_1_deg 6.454 r_scbond_it 3.541 r_mcangle_it 2.739 r_mcbond_it 2.123 r_mcbond_other 2.119 r_angle_refined_deg 1.97 r_angle_other_deg 0.912 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other 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 640 Heterogen Atoms 121
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing