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X-ray structure obtained upon reaction of dirhodium tetraacetate with RNase A (low 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% PEG4K
10 mM sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2 38.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.66 α = 90 b = 32.44 β = 92.92 c = 68.02 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 1.8 67.93 94.9 0.099 0.112 0.051 0.99 8.8 4.6 19347 16.6
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 1.8 1.84 92.9 0.256 0.294 0.14 0.854 3.4 4.4
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 NONE 4ot4 1.8 67.93 19319 993 94.12 0.172 0.1694 0.178 0.2185 0.2256 23.197
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] -1.082 0.356 1.19 -0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.706 r_dihedral_angle_3_deg 13.515 r_dihedral_angle_4_deg 11.947 r_dihedral_angle_1_deg 7.279 r_lrange_it 6.451 r_lrange_other 6.437 r_scangle_it 4.105 r_scangle_other 4.104 r_mcangle_it 3.308 r_mcangle_other 3.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.706 r_dihedral_angle_3_deg 13.515 r_dihedral_angle_4_deg 11.947 r_dihedral_angle_1_deg 7.279 r_lrange_it 6.451 r_lrange_other 6.437 r_scangle_it 4.105 r_scangle_other 4.104 r_mcangle_it 3.308 r_mcangle_other 3.308 r_scbond_it 2.647 r_scbond_other 2.646 r_mcbond_it 2.171 r_mcbond_other 2.138 r_angle_refined_deg 1.598 r_angle_other_deg 1.42 r_symmetry_nbd_refined 0.274 r_metal_ion_refined 0.27 r_xyhbond_nbd_refined 0.209 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.198 r_symmetry_nbd_other 0.182 r_nbd_other 0.165 r_nbtor_refined 0.157 r_symmetry_xyhbond_nbd_other 0.121 r_symmetry_nbtor_other 0.08 r_chiral_restr 0.077 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1867 Nucleic Acid Atoms Solvent Atoms 318 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction autoPROC data scaling PHASER phasing