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X-ray structure of the adduct formed upon reaction of dirhodium-tetraacetate with lysozyme at body temperature
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 310 2.0 M sodium formate, 0.1 M hepes buffer pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.43 α = 90 b = 80.43 β = 90 c = 36.14 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 310 PIXEL DECTRIS PILATUS 6M 2024-11-20 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) 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 2.12 56.873 94 0.092 0.998 13.2 11.4 6617
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.15 100 2.788 0.405 0.9 11.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.12 56.873 6515 332 91.4 0.201 0.1977 0.203 0.2612 0.2601 61.2
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] -0.172 -0.172 0.344
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.665 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 17.175 r_lrange_it 10.548 r_lrange_other 10.444 r_scangle_it 9.512 r_scangle_other 8.783 r_dihedral_angle_1_deg 7.25 r_mcangle_it 6.348 r_mcangle_other 6.084
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.665 r_dihedral_angle_4_deg 19.493 r_dihedral_angle_3_deg 17.175 r_lrange_it 10.548 r_lrange_other 10.444 r_scangle_it 9.512 r_scangle_other 8.783 r_dihedral_angle_1_deg 7.25 r_mcangle_it 6.348 r_mcangle_other 6.084 r_scbond_it 5.656 r_scbond_other 5.645 r_mcbond_it 4.561 r_mcbond_other 4.554 r_angle_refined_deg 1.571 r_angle_other_deg 1.355 r_nbd_refined 0.23 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.191 r_nbd_other 0.188 r_xyhbond_nbd_refined 0.184 r_nbtor_refined 0.166 r_ext_dist_refined_d 0.133 r_symmetry_xyhbond_nbd_refined 0.102 r_symmetry_nbtor_other 0.078 r_chiral_restr 0.069 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_symmetry_xyhbond_nbd_other 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement autoPROC data reduction autoPROC data scaling PHASER phasing