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The x-ray structure of bovine pancreatic ribonuclease in complex with a five-coordinate platinum(II) compound containing a sugar ligand
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 22% PEG 4K
0.01 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.78 α = 90 b = 32.519 β = 90.19 c = 72.337 γ = 90
Symmetry Space Group C 1 2 1
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 RIGAKU SATURN 944 2017-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.14 72.34 95.5 0.045 0.034 0.998 8.7 2.4 80973
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.14 1.18 92.5 0.805 0.363 0.9 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 THROUGHOUT 1.14 72.34 76770 4171 95.08 0.14123 0.13826 0.1453 0.1944 0.1946 RANDOM 26.744
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] -0.88 1.37 -1.59 2.46
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.97 r_dihedral_angle_2_deg 35.848 r_sphericity_bonded 24.248 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_4_deg 12.439 r_long_range_B_refined 11.148 r_long_range_B_other 11.148 r_mcangle_it 7.971 r_mcangle_other 7.968 r_dihedral_angle_1_deg 6.936
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.97 r_dihedral_angle_2_deg 35.848 r_sphericity_bonded 24.248 r_dihedral_angle_3_deg 14.406 r_dihedral_angle_4_deg 12.439 r_long_range_B_refined 11.148 r_long_range_B_other 11.148 r_mcangle_it 7.971 r_mcangle_other 7.968 r_dihedral_angle_1_deg 6.936 r_mcbond_other 6.856 r_mcbond_it 6.853 r_rigid_bond_restr 6.265 r_scangle_other 6.094 r_scbond_other 5.511 r_scbond_it 5.49 r_angle_refined_deg 2.534 r_angle_other_deg 1.847 r_chiral_restr 0.153 r_bond_refined_d 0.028 r_gen_planes_refined 0.014 r_gen_planes_other 0.008 r_bond_other_d 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 540 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing