☰ Navigation Tabs
X-ray structure obtained upon reaction of dirhodium tetraacetate with RNase A (high resolution)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OT4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.1 298 22% PEG 4K
10 mM sodium citrate buffer pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.18 43.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.43 α = 90 b = 32.75 β = 90.38 c = 72.69 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 PILATUS3 S 6M 2019-06-01 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 1.4 72.69 93.4 0.066 0.08 0.055 0.99 8.5 2.6 43787 12.6
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 1.4 1.42 91.3 0.259 0.327 0.196 0.861 2.4 2.2
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 NONE 4ot4 1.4 72.688 43756 2317 92.735 0.19 0.1876 0.1956 0.2326 0.2412 20.561
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] -0.069 0.074 0.025 0.042
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_3_deg 13.298 r_dihedral_angle_4_deg 9.41 r_dihedral_angle_1_deg 7.496 r_lrange_it 6.44 r_lrange_other 6.309 r_scangle_it 3.76 r_scangle_other 3.759 r_mcangle_it 3.424 r_mcangle_other 3.423
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.284 r_dihedral_angle_3_deg 13.298 r_dihedral_angle_4_deg 9.41 r_dihedral_angle_1_deg 7.496 r_lrange_it 6.44 r_lrange_other 6.309 r_scangle_it 3.76 r_scangle_other 3.759 r_mcangle_it 3.424 r_mcangle_other 3.423 r_scbond_it 2.425 r_scbond_other 2.424 r_mcbond_it 2.197 r_mcbond_other 2.174 r_angle_refined_deg 1.799 r_angle_other_deg 1.508 r_metal_ion_refined 0.462 r_nbd_refined 0.221 r_symmetry_nbd_refined 0.216 r_nbd_other 0.19 r_symmetry_nbd_other 0.189 r_symmetry_xyhbond_nbd_refined 0.176 r_nbtor_refined 0.165 r_xyhbond_nbd_refined 0.164 r_symmetry_nbtor_other 0.083 r_chiral_restr 0.081 r_symmetry_xyhbond_nbd_other 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1902 Nucleic Acid Atoms Solvent Atoms 295 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALEPACK data scaling PHASER phasing