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X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (1)
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 0.1M sodium acetate, 20% ethylene glicol, 0.6 M sodium nitrate
Crystal Properties Matthews coefficient Solvent content 1.98 37.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.964 α = 90 b = 77.964 β = 90 c = 37.291 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 CCD RIGAKU SATURN 944 2016-07-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 1.94 25.48 99 0.095 0.045 0.997 14.9 5.3 8895
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 1.94 1.97 0.44 0.249 0.808 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 193l 1.94 25.48 8875 430 99.162 0.159 0.1562 0.1647 0.2174 0.2224 21.212
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] -0.299 -0.299 0.598
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.34 r_dihedral_angle_4_deg 16.344 r_dihedral_angle_3_deg 12.039 r_dihedral_angle_1_deg 6.989 r_lrange_it 5.886 r_lrange_other 5.884 r_scangle_it 3.896 r_scangle_other 3.894 r_scbond_it 2.526 r_scbond_other 2.524
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.34 r_dihedral_angle_4_deg 16.344 r_dihedral_angle_3_deg 12.039 r_dihedral_angle_1_deg 6.989 r_lrange_it 5.886 r_lrange_other 5.884 r_scangle_it 3.896 r_scangle_other 3.894 r_scbond_it 2.526 r_scbond_other 2.524 r_angle_refined_deg 2.384 r_mcangle_it 2.088 r_mcangle_other 2.085 r_mcbond_it 1.576 r_angle_other_deg 1.51 r_mcbond_other 1.443 r_nbd_other 0.309 r_symmetry_xyhbond_nbd_refined 0.255 r_xyhbond_nbd_refined 0.24 r_nbd_refined 0.224 r_symmetry_nbd_other 0.21 r_symmetry_nbd_refined 0.189 r_nbtor_refined 0.161 r_symmetry_xyhbond_nbd_other 0.145 r_ext_dist_refined_d 0.13 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.084 r_metal_ion_refined 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 126 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing