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The crystal structure of Sporosarcina pasteurii urease in complex with citrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1S3T PDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.3 1.8 M AMMONIUM SULPHATE, 100 MM CITRATE PH 6.3, 50 MM NA2SO3
Crystal Properties Matthews coefficient Solvent content 2.76 55.46
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.555 α = 90 b = 131.555 β = 90 c = 189.521 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 2011-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) PETRA III, EMBL c/o DESY P14 (MX2)
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 1.5 113.93 99.9 0.1 22.6 15.5 153738 2
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 1.5 1.58 100 0.58 4 9.9
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1S3T DEPLETED OF WATERS SULPHATES AND BORATE WAS USED AS A MODEL FOR RIGID BODY REFINEMENT FOLLOWED BY REFINEMENT AND MODEL BUILDING 1.5 113.93 145792 7712 99.86 0.11847 0.11703 0.13 0.14605 0.1564 RANDOM 13.109
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_sphericity_free 24.641 r_dihedral_angle_4_deg 16.322 r_dihedral_angle_3_deg 11.53 r_sphericity_bonded 7.086 r_dihedral_angle_1_deg 6.259 r_rigid_bond_restr 2.383 r_angle_refined_deg 1.448 r_angle_other_deg 0.947 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.847 r_sphericity_free 24.641 r_dihedral_angle_4_deg 16.322 r_dihedral_angle_3_deg 11.53 r_sphericity_bonded 7.086 r_dihedral_angle_1_deg 6.259 r_rigid_bond_restr 2.383 r_angle_refined_deg 1.448 r_angle_other_deg 0.947 r_chiral_restr 0.087 r_bond_refined_d 0.01 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6014 Nucleic Acid Atoms Solvent Atoms 671 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling REFMAC phasing