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Unexpected imidazole coordination to dirhodium tetraacetate complex in a protein environment: insights from X-ray crystallography and quantum chemistry
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 4000
10 mM sodium citrate pH 5.1
Crystal Properties Matthews coefficient Solvent content 2.15 42.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.5 α = 90 b = 32.53 β = 90.295 c = 72.2 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 2021-03-03 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) Rrim 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 50.3 94.3 0.058 1 15.4 6.4 43550
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.43 87.91 1.079 0.8 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 FREE R-VALUE 1JVT 1.4 50.3 43550 2039 94.3 0.192 0.1897 0.1901 0.231 0.2313 24.977
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] -0.139 0.101 -0.14 0.278
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.674 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_3_deg 13.801 r_lrange_it 7.546 r_lrange_other 7.54 r_dihedral_angle_1_deg 7.203 r_scangle_it 4.65 r_scangle_other 4.566 r_angle_refined_deg 3.948 r_mcangle_it 3.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.674 r_dihedral_angle_4_deg 14.44 r_dihedral_angle_3_deg 13.801 r_lrange_it 7.546 r_lrange_other 7.54 r_dihedral_angle_1_deg 7.203 r_scangle_it 4.65 r_scangle_other 4.566 r_angle_refined_deg 3.948 r_mcangle_it 3.747 r_mcangle_other 3.746 r_scbond_it 3.147 r_scbond_other 3.105 r_mcbond_it 2.527 r_mcbond_other 2.527 r_angle_other_deg 1.517 r_symmetry_xyhbond_nbd_refined 0.237 r_nbd_other 0.204 r_nbd_refined 0.203 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.18 r_symmetry_nbd_refined 0.177 r_nbtor_refined 0.167 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.084 r_bond_refined_d 0.014 r_gen_planes_refined 0.013 r_gen_planes_other 0.004 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1898 Nucleic Acid Atoms Solvent Atoms 261 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement AutoProcess data reduction AutoProcess data scaling PHASER phasing