☰ Navigation Tabs
X-ray structure of the adduct formed upon reaction of RNase A with [Ru2Cl(D-p-CNPhF)(O2CCH3)3]
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 Free-interface diffusion of a 10 uL of 30 mg/ml protein solution, 20 mM sodium citrate at pH 5.3 agaist 10 ul isopropanol 99.9% isopropanol
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.62 α = 90 b = 32.74 β = 90.29 c = 72.25 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 2022-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.0 ELETTRA 11.2C
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 1.4 72.25 91 0.048 0.999 19.4 5.6 36934
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 1.4 1.53 0.494 0.82 2.2
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 1.4 72.249 36934 1758 78.803 0.176 0.1745 0.1844 0.2143 0.2203 19.483
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] 0.001 -0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.178 r_dihedral_angle_3_deg 11.478 r_lrange_it 8.439 r_lrange_other 8.383 r_dihedral_angle_1_deg 7.041 r_scangle_other 4.445 r_scangle_it 4.393 r_dihedral_angle_2_deg 4.073 r_mcangle_it 4.041 r_mcangle_other 4.039
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.178 r_dihedral_angle_3_deg 11.478 r_lrange_it 8.439 r_lrange_other 8.383 r_dihedral_angle_1_deg 7.041 r_scangle_other 4.445 r_scangle_it 4.393 r_dihedral_angle_2_deg 4.073 r_mcangle_it 4.041 r_mcangle_other 4.039 r_scbond_other 2.802 r_scbond_it 2.792 r_mcbond_it 2.539 r_mcbond_other 2.539 r_angle_refined_deg 1.756 r_angle_other_deg 0.607 r_nbd_refined 0.212 r_symmetry_nbd_other 0.2 r_symmetry_nbd_refined 0.2 r_nbd_other 0.185 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_other 0.159 r_xyhbond_nbd_refined 0.157 r_chiral_restr 0.087 r_symmetry_nbtor_other 0.084 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1894 Nucleic Acid Atoms Solvent Atoms 308 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing