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Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (4)
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 4.5 293 0.1 M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.01 38.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.604 α = 90 b = 78.604 β = 90 c = 37.307 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 100 PIXEL DECTRIS PILATUS 6M-F 2020-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.32 55.58 95.4 0.047 0.013 1 28.8 25.8 26513
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 1.32 1.37 51.1 2.55 0.72 0.612 25.9
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 193l 1.32 55.58 26513 1286 95.384 0.18 0.1777 0.1872 0.2233 0.2281 27.339
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] -0.011 -0.011 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_4_deg 19.989 r_dihedral_angle_3_deg 12.66 r_lrange_it 7.461 r_lrange_other 7.329 r_dihedral_angle_1_deg 6.438 r_scangle_it 5.514 r_scangle_other 5.511 r_scbond_it 3.704 r_scbond_other 3.704
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.632 r_dihedral_angle_4_deg 19.989 r_dihedral_angle_3_deg 12.66 r_lrange_it 7.461 r_lrange_other 7.329 r_dihedral_angle_1_deg 6.438 r_scangle_it 5.514 r_scangle_other 5.511 r_scbond_it 3.704 r_scbond_other 3.704 r_mcangle_other 2.672 r_mcangle_it 2.66 r_angle_refined_deg 2.394 r_mcbond_it 2.324 r_mcbond_other 1.978 r_angle_other_deg 1.643 r_nbd_refined 0.252 r_nbd_other 0.248 r_ext_dist_refined_d 0.247 r_symmetry_xyhbond_nbd_refined 0.242 r_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.214 r_xyhbond_nbd_other 0.201 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.156 r_symmetry_xyhbond_nbd_other 0.136 r_metal_ion_refined 0.104 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.088 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.009 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 96
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOSFLM data scaling PHASER phasing