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X-ray structure of the adduct formed upon reaction of ribonuclease A with a tetranuclear Pt-thiosemicarbazone compound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 22% PEG4K
0.01 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.15 42.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.951 α = 90 b = 32.584 β = 89.35 c = 72.502 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 A200 2017-04-04 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) 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 1.78 72.5 97.9 0.071 0.047 22.5 2.8 22108 62971
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.78 1.82 76 0.766 0.75 1.3 1
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 MOLECULAR REPLACEMENT THROUGHOUT 1JVT 1.78 72.5 21079 1026 96.98 0.19827 0.19578 0.2022 0.25043 0.256 RANDOM 35.726
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] 0.34 -0.36 -0.24 -0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_3_deg 14.606 r_dihedral_angle_4_deg 13.336 r_dihedral_angle_1_deg 7.268 r_long_range_B_refined 7.208 r_long_range_B_other 7.153 r_scangle_other 5.376 r_mcangle_it 4.368 r_mcangle_other 4.367 r_scbond_it 3.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.343 r_dihedral_angle_3_deg 14.606 r_dihedral_angle_4_deg 13.336 r_dihedral_angle_1_deg 7.268 r_long_range_B_refined 7.208 r_long_range_B_other 7.153 r_scangle_other 5.376 r_mcangle_it 4.368 r_mcangle_other 4.367 r_scbond_it 3.55 r_scbond_other 3.55 r_mcbond_other 3.169 r_mcbond_it 3.168 r_angle_refined_deg 2.273 r_angle_other_deg 1.084 r_chiral_restr 0.107 r_bond_refined_d 0.016 r_gen_planes_refined 0.016 r_bond_other_d 0.004 r_gen_planes_other 0.002 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1901 Nucleic Acid Atoms Solvent Atoms 209 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing