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1.59 A resolution Fluoride 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 6.5 1.8 M AMMONIUM SULPHATE, 50 MM SODIUM SULPHITE, 50 MM SODIUM CITRATE, 100 MM SODIUM FLUORIDE, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.73 55.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.331 α = 90 b = 131.331 β = 90 c = 188.882 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 CCD MARRESEARCH 2012-06-19 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 1.59 113.74 100 0.1 19.7 14.4 128776 2 12.3
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 1.59 1.63 100 0.52 4.6 8.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 1.589 113.736 2 128593 6458 99.808 0.131 0.1297 0.1448 0.1502 0.163 RANDOM 13.824
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] 0.372 0.372 0.372 -1.207
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 17.742 r_dihedral_angle_3_deg 11.944 r_dihedral_angle_1_deg 6.287 r_scangle_it 5.581 r_scbond_it 3.388 r_mcangle_it 1.845 r_angle_refined_deg 1.53 r_mcbond_it 1.167 r_angle_other_deg 0.822
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.076 r_dihedral_angle_4_deg 17.742 r_dihedral_angle_3_deg 11.944 r_dihedral_angle_1_deg 6.287 r_scangle_it 5.581 r_scbond_it 3.388 r_mcangle_it 1.845 r_angle_refined_deg 1.53 r_mcbond_it 1.167 r_angle_other_deg 0.822 r_nbd_refined 0.264 r_mcbond_other 0.247 r_nbd_other 0.187 r_nbtor_refined 0.176 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_other 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_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 6014 Nucleic Acid Atoms Solvent Atoms 826 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling