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X-ray structure of the adduct formed upon reaction of a vanadium hydroxyquinoline complex 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 5.1 293 22% PEG4K, 10 mM sodium citrate buffer pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.74 α = 90 b = 32.47 β = 90.511 c = 72.86 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 2021-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 0.96 ELETTRA 11.2C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.573 50.368 99 0.04 0.044 0.018 0.999 21.6 6 33104
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.573 1.6 92.9 0.725 0.826 0.384 0.645 2.2 4.5
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 1.573 50.368 33104 1553 98.951 0.176 0.1742 0.1842 0.2223 0.2326 30.521
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] -0.055 0.122 0.03 0.023
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_3_deg 15.55 r_dihedral_angle_4_deg 12.976 r_lrange_it 7.357 r_lrange_other 7.23 r_dihedral_angle_1_deg 7.051 r_scangle_other 5.226 r_scangle_it 5.215 r_mcangle_other 4.294 r_mcangle_it 4.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.035 r_dihedral_angle_3_deg 15.55 r_dihedral_angle_4_deg 12.976 r_lrange_it 7.357 r_lrange_other 7.23 r_dihedral_angle_1_deg 7.051 r_scangle_other 5.226 r_scangle_it 5.215 r_mcangle_other 4.294 r_mcangle_it 4.293 r_scbond_it 3.368 r_scbond_other 3.367 r_mcbond_it 2.872 r_mcbond_other 2.866 r_angle_refined_deg 1.736 r_angle_other_deg 1.508 r_nbd_other 0.218 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.184 r_symmetry_nbd_other 0.183 r_symmetry_xyhbond_nbd_refined 0.168 r_nbtor_refined 0.165 r_symmetry_xyhbond_nbd_other 0.134 r_symmetry_nbd_refined 0.127 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.076 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing