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X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] with RNase A (2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JVT
Crystallization Crystalization Experiments ID Method pH Temperature Details 2 VAPOR DIFFUSION, HANGING DROP 5.1 298 22% PEG 4K
10 mM sodium citrate buffer pH 5.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.21 α = 90 b = 32.56 β = 90.309 c = 72.61 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 1.32 41.143 99.5 0.138 0.1 0.996 10.8 5.5 54908
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 1.32 1.35 100 0.862 0.57 0.704 2.2 5.8
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 1.32 41.14 54908 2648 99.471 0.21 0.2088 0.2169 0.243 0.2515 15.86
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] -0.032 0.036 0.062 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.654 r_dihedral_angle_3_deg 14.29 r_dihedral_angle_4_deg 11.66 r_dihedral_angle_1_deg 7.654 r_lrange_it 4.998 r_lrange_other 4.748 r_angle_refined_deg 3.098 r_scangle_it 2.855 r_scangle_other 2.85 r_mcangle_it 2.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.654 r_dihedral_angle_3_deg 14.29 r_dihedral_angle_4_deg 11.66 r_dihedral_angle_1_deg 7.654 r_lrange_it 4.998 r_lrange_other 4.748 r_angle_refined_deg 3.098 r_scangle_it 2.855 r_scangle_other 2.85 r_mcangle_it 2.36 r_mcangle_other 2.359 r_scbond_it 1.905 r_scbond_other 1.884 r_angle_other_deg 1.545 r_mcbond_it 1.525 r_mcbond_other 1.525 r_nbd_refined 0.198 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.183 r_symmetry_nbd_refined 0.173 r_xyhbond_nbd_refined 0.169 r_nbd_other 0.167 r_nbtor_refined 0.165 r_symmetry_nbtor_other 0.084 r_chiral_restr 0.082 r_symmetry_xyhbond_nbd_other 0.08 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 387 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction AutoProcess data scaling PHASER phasing