☰ Navigation Tabs
X-ray structure of the adduct formed upon reaction of the organopalladium compound complex 2 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 298 22% PEG 4K, 10 mM sodium citrate buffer pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.21 44.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.465 α = 90 b = 32.852 β = 90.441 c = 72.55 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 0.87313 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 2.72 50.73 99.7 0.158 0.979 5.2 5 6663
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 2.72 2.77 99.7 3.708 0.441 0.8 5.1
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 2.72 50.73 6635 300 99.267 0.218 0.216 0.221 0.2585 0.2623 95.478
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] -6.11 -1.356 2.634 3.496
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.907 r_dihedral_angle_3_deg 14.289 r_lrange_other 14.021 r_lrange_it 14.01 r_mcangle_other 10.447 r_mcangle_it 10.443 r_scangle_it 9.637 r_scangle_other 9.366 r_dihedral_angle_4_deg 9.258 r_dihedral_angle_1_deg 7.165
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.907 r_dihedral_angle_3_deg 14.289 r_lrange_other 14.021 r_lrange_it 14.01 r_mcangle_other 10.447 r_mcangle_it 10.443 r_scangle_it 9.637 r_scangle_other 9.366 r_dihedral_angle_4_deg 9.258 r_dihedral_angle_1_deg 7.165 r_mcbond_it 6.572 r_mcbond_other 6.558 r_scbond_it 6.145 r_scbond_other 5.808 r_angle_refined_deg 1.523 r_angle_other_deg 1.197 r_nbd_other 0.215 r_nbd_refined 0.21 r_symmetry_nbd_other 0.198 r_metal_ion_refined 0.192 r_symmetry_xyhbond_nbd_refined 0.155 r_nbtor_refined 0.153 r_symmetry_nbd_refined 0.144 r_xyhbond_nbd_refined 0.143 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.051 r_symmetry_xyhbond_nbd_other 0.039 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing