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Crystal structure of hen egg white lysozyme at 100 Kelvin with Lard (Duplicate)
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 1.99 38.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.442 α = 90 b = 78.442 β = 90 c = 37.166 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 22.227 99.604 0.99 18 1 19130
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 22.227 19130 943 99.604 0.214 0.2125 0.2205 0.245 0.2475 9.633
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] -0.006 -0.006 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.07 r_dihedral_angle_3_deg 11.401 r_dihedral_angle_2_deg 8.054 r_dihedral_angle_1_deg 6.626 r_lrange_it 4.094 r_lrange_other 4.031 r_scangle_it 2.895 r_scangle_other 2.893 r_scbond_it 1.834 r_scbond_other 1.833
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.07 r_dihedral_angle_3_deg 11.401 r_dihedral_angle_2_deg 8.054 r_dihedral_angle_1_deg 6.626 r_lrange_it 4.094 r_lrange_other 4.031 r_scangle_it 2.895 r_scangle_other 2.893 r_scbond_it 1.834 r_scbond_other 1.833 r_angle_refined_deg 1.796 r_mcangle_other 1.748 r_mcangle_it 1.746 r_mcbond_it 1.098 r_mcbond_other 1.096 r_angle_other_deg 0.645 r_xyhbond_nbd_refined 0.381 r_nbd_refined 0.256 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.183 r_nbd_other 0.152 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.078 r_symmetry_nbd_refined 0.061 r_symmetry_xyhbond_nbd_refined 0.033 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 96 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement