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X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (3)
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 38.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.36 α = 90 b = 78.36 β = 90 c = 37.61 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 2019-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 11.2C 1.5406 ELETTRA 11.2C
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 1.4 78.36 100 0.099 0.023 0.999 10.2 19.6 23665
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 1.4 1.47 100 2 0.519 0.701 16.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 193L 1.4 55.409 23665 1212 99.97 0.191 0.1901 0.1905 0.2089 0.2093 16.827
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] -0.347 -0.347 0.694
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_3_deg 14.973 r_dihedral_angle_4_deg 14.543 r_lrange_it 6.85 r_lrange_other 6.653 r_dihedral_angle_1_deg 6.515 r_scangle_it 4.249 r_scangle_other 4.247 r_scbond_it 2.801 r_scbond_other 2.798
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.339 r_dihedral_angle_3_deg 14.973 r_dihedral_angle_4_deg 14.543 r_lrange_it 6.85 r_lrange_other 6.653 r_dihedral_angle_1_deg 6.515 r_scangle_it 4.249 r_scangle_other 4.247 r_scbond_it 2.801 r_scbond_other 2.798 r_mcangle_other 2.168 r_mcangle_it 2.162 r_angle_refined_deg 1.866 r_angle_other_deg 1.644 r_mcbond_it 1.556 r_mcbond_other 1.466 r_nbd_other 0.27 r_nbd_refined 0.252 r_ext_dist_refined_d 0.24 r_xyhbond_nbd_refined 0.239 r_symmetry_nbd_other 0.209 r_symmetry_xyhbond_nbd_refined 0.194 r_nbtor_refined 0.171 r_symmetry_nbd_refined 0.158 r_chiral_restr 0.102 r_metal_ion_refined 0.097 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_other 0.074 r_bond_refined_d 0.013 r_gen_planes_refined 0.012 r_bond_other_d 0.008 r_xyhbond_nbd_other 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 88
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOSFLM data scaling PHASER phasing