☰ Navigation Tabs
X-ray structure of the adduct obtained upon reaction of [cis-Rh2(OCOCH3)2(OCOCF3)2] 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 22 % PEG 4K
0.01 M sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.22 44.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.5 α = 90 b = 32.91 β = 90.164 c = 73.06 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 1.15 73.06 99.6 0.078 0.051 0.997 10.3 6.1 84723
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 1.15 1.17 100 0.699 0.479 0.738 2.2 5.4
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 1.15 73.06 84723 4156 99.6 0.137 0.136 0.1354 0.1654 0.1664 17.985
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] -0.771 0.508 0.268 0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_3_deg 12.296 r_dihedral_angle_4_deg 11.199 r_rigid_bond_restr 7.571 r_dihedral_angle_1_deg 7.34 r_lrange_it 6.318 r_lrange_other 5.841 r_scangle_it 5.537 r_scangle_other 5.537 r_scbond_it 4.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.841 r_dihedral_angle_3_deg 12.296 r_dihedral_angle_4_deg 11.199 r_rigid_bond_restr 7.571 r_dihedral_angle_1_deg 7.34 r_lrange_it 6.318 r_lrange_other 5.841 r_scangle_it 5.537 r_scangle_other 5.537 r_scbond_it 4.735 r_scbond_other 4.731 r_mcangle_it 4.315 r_mcangle_other 4.313 r_mcbond_other 4.3 r_mcbond_it 4.298 r_angle_refined_deg 3.404 r_angle_other_deg 1.659 r_nbd_refined 0.285 r_nbd_other 0.23 r_symmetry_nbd_other 0.214 r_symmetry_nbd_refined 0.206 r_xyhbond_nbd_refined 0.177 r_nbtor_refined 0.173 r_symmetry_xyhbond_nbd_refined 0.167 r_chiral_restr 0.11 r_symmetry_nbtor_other 0.09 r_bond_refined_d 0.018 r_symmetry_xyhbond_nbd_other 0.016 r_gen_planes_refined 0.014 r_gen_planes_other 0.005 r_bond_other_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1881 Nucleic Acid Atoms Solvent Atoms 489 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction AutoProcess data scaling PHASER phasing