☰ Navigation Tabs
Unusual structural features in the adduct of dirhodium tetraacetate with lysozyme (5)
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, 0.1 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 2.01 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.7 α = 90 b = 78.7 β = 90 c = 37.245 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 1.74 35.19 91.1 0.07 0.02 1 24.7 25 11349
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 1.74 1.83 36 3.12 0.848 0.474 1.1 27.6
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 193L 1.74 35.19 11349 555 90.756 0.187 0.1847 0.2284 0.2537 42.938
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] -0.227 -0.227 0.455
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.207 r_dihedral_angle_4_deg 18.595 r_dihedral_angle_3_deg 14.871 r_lrange_other 9.528 r_lrange_it 9.527 r_dihedral_angle_1_deg 7.122 r_scangle_it 7.037 r_scangle_other 7.032 r_scbond_it 4.462 r_scbond_other 4.459
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.207 r_dihedral_angle_4_deg 18.595 r_dihedral_angle_3_deg 14.871 r_lrange_other 9.528 r_lrange_it 9.527 r_dihedral_angle_1_deg 7.122 r_scangle_it 7.037 r_scangle_other 7.032 r_scbond_it 4.462 r_scbond_other 4.459 r_mcangle_other 3.977 r_mcangle_it 3.969 r_mcbond_it 3.025 r_mcbond_other 3.006 r_angle_refined_deg 1.553 r_angle_other_deg 1.384 r_xyhbond_nbd_refined 0.228 r_nbd_refined 0.222 r_nbd_other 0.194 r_symmetry_nbd_other 0.191 r_ext_dist_refined_d 0.19 r_symmetry_xyhbond_nbd_refined 0.171 r_symmetry_nbd_refined 0.166 r_nbtor_refined 0.159 r_metal_ion_refined 0.093 r_symmetry_nbtor_other 0.081 r_chiral_restr 0.079 r_xyhbond_nbd_other 0.025 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 75 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOSFLM data scaling PHASER phasing