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X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (4)
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
0.01 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.22 44.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.73 α = 90 b = 32.87 β = 90.154 c = 72.89 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 PILATUS 6M 2021-05-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.00 ELETTRA 11.2C
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 1.45 50.86 99.9 0.185 0.135 0.988 11.8 5.2 43428
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 100 0.796 0.557 0.67 3.1 5.6
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 1JVT 1.45 50.855 42535 2090 99.256 0.164 0.1619 0.1618 0.2019 0.2018 16.092
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] -0.026 0.052 0.053 -0.027
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_4_deg 12.896 r_dihedral_angle_1_deg 7.769 r_lrange_it 7.44 r_lrange_other 7.201 r_scangle_other 3.481 r_scangle_it 3.458 r_mcangle_it 2.878 r_mcangle_other 2.877
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.731 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_4_deg 12.896 r_dihedral_angle_1_deg 7.769 r_lrange_it 7.44 r_lrange_other 7.201 r_scangle_other 3.481 r_scangle_it 3.458 r_mcangle_it 2.878 r_mcangle_other 2.877 r_angle_refined_deg 2.801 r_scbond_it 2.282 r_scbond_other 2.265 r_mcbond_it 1.768 r_mcbond_other 1.768 r_angle_other_deg 1.549 r_nbd_refined 0.238 r_symmetry_xyhbond_nbd_other 0.225 r_symmetry_nbd_other 0.188 r_xyhbond_nbd_refined 0.183 r_nbd_other 0.18 r_nbtor_refined 0.17 r_symmetry_xyhbond_nbd_refined 0.147 r_symmetry_nbd_refined 0.132 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1882 Nucleic Acid Atoms Solvent Atoms 436 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction AutoProcess data scaling PHASER phasing