☰ Navigation Tabs
X-ray structure of the adduct obtained upon reaction of [Rh2(OCOCH3)(OCOCF3)3] with RNase A (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 5.1 298 0.01 M sodium citrate pH 5.1;
22% PEG 4K
Crystal Properties Matthews coefficient Solvent content 2.26 45.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 101.69 α = 90 b = 33.12 β = 90.133 c = 73.45 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 1.45 50.85 99 0.185 0.135 0.998 11.8 5.2 43428
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 1.45 1.48 100 0.796 0.557 0.67 3.1 5.6
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 1.45 50.85 43428 2106 99.011 0.203 0.2015 0.2015 0.2321 0.2324 19.079
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] -0.01 0.017 0.013 -0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_4_deg 11.285 r_dihedral_angle_1_deg 7.231 r_lrange_it 5.728 r_lrange_other 5.673 r_scangle_it 3.545 r_scangle_other 3.541 r_mcangle_it 3.01 r_mcangle_other 3.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.233 r_dihedral_angle_3_deg 15.351 r_dihedral_angle_4_deg 11.285 r_dihedral_angle_1_deg 7.231 r_lrange_it 5.728 r_lrange_other 5.673 r_scangle_it 3.545 r_scangle_other 3.541 r_mcangle_it 3.01 r_mcangle_other 3.009 r_scbond_it 2.336 r_scbond_other 2.321 r_mcbond_it 1.927 r_mcbond_other 1.925 r_angle_refined_deg 1.83 r_angle_other_deg 1.525 r_nbd_other 0.258 r_symmetry_nbd_refined 0.214 r_nbd_refined 0.21 r_symmetry_nbd_other 0.193 r_xyhbond_nbd_refined 0.175 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.145 r_chiral_restr 0.1 r_symmetry_nbtor_other 0.083 r_ext_dist_refined_d 0.041 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 1880 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 17
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing