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X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-PHOSPHINE COMPOUND Au(PEt3)I DETERMINED AT 1.80 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 2.77 55.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 131.645 α = 90 b = 131.645 β = 90 c = 189.2 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 1.8 114 100 0.142 0.154 0.042 0.999 17 13.2 89759 25.26
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 1.8 1.83 100 2.3 2.484 0.931 0.694 1.5 13.5
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 1.8 72.907 89704 4419 99.975 0.156 0.155 0.1568 0.1763 0.1783 31.017
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] 1.002 0.501 1.002 -3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_rigid_bond_restr 21.785 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 14.048 r_lrange_it 7.792 r_dihedral_angle_1_deg 7.187 r_scangle_it 5.945 r_scbond_it 4.443 r_mcangle_it 3.033 r_mcbond_it 2.422
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.617 r_rigid_bond_restr 21.785 r_dihedral_angle_4_deg 17.946 r_dihedral_angle_3_deg 14.048 r_lrange_it 7.792 r_dihedral_angle_1_deg 7.187 r_scangle_it 5.945 r_scbond_it 4.443 r_mcangle_it 3.033 r_mcbond_it 2.422 r_angle_refined_deg 1.747 r_nbtor_refined 0.308 r_nbd_refined 0.216 r_symmetry_nbd_refined 0.204 r_symmetry_xyhbond_nbd_refined 0.198 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.116 r_bond_refined_d 0.013 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5994 Nucleic Acid Atoms Solvent Atoms 549 Heterogen Atoms 143
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing