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Crystal structure of hen egg white lysozyme at 100 Kelvin with Glycerol 30%
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 1.2 M sodium chloride, 100 mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.98 38.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.425 α = 90 b = 78.425 β = 90 c = 36.994 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 Bruker PHOTON II 2024-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.498 22.187 99.346 0.99 18 1 18983
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.498 10 0.99
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.498 22.187 18983 937 99.346 0.203 0.2008 0.2009 0.2366 0.2371 14.147
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] 0.009 0.009 -0.018
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.987 r_dihedral_angle_6_deg 14.96 r_dihedral_angle_3_deg 11.652 r_dihedral_angle_1_deg 6.676 r_lrange_it 4.815 r_lrange_other 4.624 r_scangle_it 3.645 r_scangle_other 3.642 r_scbond_it 2.378 r_scbond_other 2.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 14.987 r_dihedral_angle_6_deg 14.96 r_dihedral_angle_3_deg 11.652 r_dihedral_angle_1_deg 6.676 r_lrange_it 4.815 r_lrange_other 4.624 r_scangle_it 3.645 r_scangle_other 3.642 r_scbond_it 2.378 r_scbond_other 2.375 r_mcangle_other 1.928 r_mcangle_it 1.925 r_angle_refined_deg 1.76 r_mcbond_it 1.339 r_mcbond_other 1.294 r_angle_other_deg 0.615 r_xyhbond_nbd_refined 0.382 r_nbd_refined 0.259 r_symmetry_xyhbond_nbd_refined 0.221 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.182 r_nbd_other 0.163 r_metal_ion_refined 0.156 r_symmetry_nbd_refined 0.103 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.009 r_gen_planes_refined 0.009 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 95 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement