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X-ray structure of the adduct formed upon reaction of the organopalladium compound complex 1 with RNase A
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 5.1 298 22% PEG 4K, 10 mM sodium citrate buffer pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.26 45.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.02 α = 90 b = 32.863 β = 90.509 c = 74.644 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 PIXEL DECTRIS EIGER X 9M 2025-01-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.87 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.99 31.25 72.8 0.169 0.982 5.7 3 12608
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.99 2.02 77.6 1.55 0.333 1.5 2.9
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.99 31.25 12331 644 71.24 0.212 0.211 0.2193 0.2343 0.2425 42.265
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] -1.769 -0.33 -0.199 1.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.278 r_dihedral_angle_4_deg 15.857 r_dihedral_angle_3_deg 13.678 r_lrange_other 7.201 r_lrange_it 7.194 r_dihedral_angle_1_deg 7.071 r_mcangle_it 4.691 r_mcangle_other 4.69 r_scangle_it 4.499 r_scangle_other 4.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.278 r_dihedral_angle_4_deg 15.857 r_dihedral_angle_3_deg 13.678 r_lrange_other 7.201 r_lrange_it 7.194 r_dihedral_angle_1_deg 7.071 r_mcangle_it 4.691 r_mcangle_other 4.69 r_scangle_it 4.499 r_scangle_other 4.499 r_mcbond_it 2.915 r_mcbond_other 2.915 r_scbond_it 2.86 r_scbond_other 2.857 r_angle_refined_deg 1.537 r_angle_other_deg 1.277 r_nbd_other 0.246 r_symmetry_nbd_other 0.195 r_nbd_refined 0.193 r_symmetry_xyhbond_nbd_refined 0.167 r_xyhbond_nbd_refined 0.166 r_symmetry_nbd_refined 0.159 r_nbtor_refined 0.156 r_symmetry_xyhbond_nbd_other 0.133 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.061 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 84 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing