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X-ray structure of the adduct of a vanadium picolinate complex with RNase A at pH 5.1
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% PEG 4K
10 mM sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.19 43.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.23 α = 90 b = 33.02 β = 90.161 c = 72.71 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 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 1.268 72.71 91.3 0.095 0.105 0.042 0.992 8.6 5 58090
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 1.268 1.29 79.8 0.664 0.761 0.365 0.828 2.1 4.2
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 1.27 72.71 57790 2754 91.291 0.161 0.158 0.159 0.2222 0.2235 20.638
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] -1.101 -0.021 0.651 0.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.638 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_4_deg 13.521 r_dihedral_angle_1_deg 6.79 r_lrange_it 5.549 r_lrange_other 5.285 r_scangle_it 5.052 r_scangle_other 4.95 r_scbond_it 4.49 r_scbond_other 4.446
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.638 r_dihedral_angle_3_deg 13.551 r_dihedral_angle_4_deg 13.521 r_dihedral_angle_1_deg 6.79 r_lrange_it 5.549 r_lrange_other 5.285 r_scangle_it 5.052 r_scangle_other 4.95 r_scbond_it 4.49 r_scbond_other 4.446 r_mcangle_it 4.143 r_mcangle_other 4.142 r_rigid_bond_restr 4.077 r_mcbond_it 3.66 r_mcbond_other 3.656 r_angle_refined_deg 3.549 r_angle_other_deg 1.621 r_nbd_other 0.238 r_nbd_refined 0.206 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.2 r_xyhbond_nbd_refined 0.196 r_symmetry_xyhbond_nbd_refined 0.192 r_xyhbond_nbd_other 0.181 r_nbtor_refined 0.168 r_chiral_restr 0.106 r_symmetry_nbtor_other 0.089 r_bond_refined_d 0.017 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1862 Nucleic Acid Atoms Solvent Atoms 389 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing