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X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-DIPHOSPHINE COMPOUND Au(PEt3)2Cl DETERMINED AT 1.87 ANGSTROMS
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 6.5 293 THE PROTEIN-LIGAND (1.2 mM) COMPLEX IN 50 MM HEPES BUFFER, PH 7.50 (ALSO CONTAINING 10% (V/V) DMSO), DILUTED 1:1 WITH A SOLUTION OF 1.2-1.7 M AMMONIUM SULFATE ALSO CONTAINING THE SAME CONCENTRATION OF LIGAND AND DMSO.
Crystal Properties Matthews coefficient Solvent content 2.76 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.797 α = 90 b = 131.797 β = 90 c = 189.381 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-F 2019-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) 0.9762 PETRA III, EMBL c/o DESY P13 (MX1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.87 114 100 0.151 0.159 0.038 0.999 17.9 17.4 80498 26.89
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.87 1.91 100 3.098 3.296 0.778 0.744 1.5 17.5
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ol4 1.87 65.985 80442 4008 99.964 0.167 0.165 0.1666 0.2103 0.2123 38.018
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] 1.357 0.679 1.357 -4.404
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.067 r_dihedral_angle_4_deg 18.889 r_rigid_bond_restr 15.674 r_dihedral_angle_3_deg 15.055 r_lrange_it 8.565 r_scangle_it 7.285 r_dihedral_angle_1_deg 7.276 r_scbond_it 5.762 r_mcangle_it 3.786 r_mcbond_it 3.268
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.067 r_dihedral_angle_4_deg 18.889 r_rigid_bond_restr 15.674 r_dihedral_angle_3_deg 15.055 r_lrange_it 8.565 r_scangle_it 7.285 r_dihedral_angle_1_deg 7.276 r_scbond_it 5.762 r_mcangle_it 3.786 r_mcbond_it 3.268 r_angle_refined_deg 1.895 r_nbtor_refined 0.314 r_nbd_refined 0.223 r_symmetry_nbd_refined 0.201 r_symmetry_xyhbond_nbd_refined 0.179 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.123 r_bond_refined_d 0.012 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5993 Nucleic Acid Atoms Solvent Atoms 469 Heterogen Atoms 150
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing