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X-ray structure of Hen Egg White Lysozyme with dirhodium tetraacetate (6)
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 7.5 293 0.01 M HEPES, 2.00 M sodium formate
Crystal Properties Matthews coefficient Solvent content 2.02 39.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.93 α = 90 b = 78.93 β = 90 c = 37.12 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 2020-11-19 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 1.65 55.812 94 0.12 0.025 1 22.5 24.5 11800
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 1.65 1.8 52.6 3.23 0.68 0.51 1.3 22.4
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 1.65 55.81 11800 595 80.601 0.185 0.1819 0.2341 0.2027 30.659
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] -0.023 -0.023 0.046
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.069 r_dihedral_angle_4_deg 23.303 r_dihedral_angle_3_deg 14.523 r_lrange_it 8.384 r_lrange_other 8.349 r_dihedral_angle_1_deg 7.409 r_scangle_it 5.727 r_scangle_other 5.723 r_mcangle_it 3.551 r_mcangle_other 3.551
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.069 r_dihedral_angle_4_deg 23.303 r_dihedral_angle_3_deg 14.523 r_lrange_it 8.384 r_lrange_other 8.349 r_dihedral_angle_1_deg 7.409 r_scangle_it 5.727 r_scangle_other 5.723 r_mcangle_it 3.551 r_mcangle_other 3.551 r_scbond_it 3.522 r_scbond_other 3.52 r_mcbond_it 2.475 r_mcbond_other 2.456 r_angle_refined_deg 1.546 r_angle_other_deg 1.411 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.201 r_nbd_other 0.199 r_symmetry_nbd_other 0.194 r_xyhbond_nbd_refined 0.172 r_nbtor_refined 0.162 r_metal_ion_refined 0.147 r_symmetry_nbd_refined 0.112 r_chiral_restr 0.079 r_symmetry_nbtor_other 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 106 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction MOSFLM data scaling PHASER phasing