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Crystal structure of hen egg white lysozyme at 100 Kelvin with PEG 400 (Triplicate)
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 NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.94 36.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.196 α = 90 b = 77.196 β = 90 c = 37.401 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 1.499 21.41 99 0.99 18 1 18625
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 1.499 21.41 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 1.5 21.41 18625 974 99.818 0.207 0.2063 0.2163 0.2171 0.2259 14.021
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] 0.002 0.002 -0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.254 r_dihedral_angle_3_deg 11.915 r_dihedral_angle_2_deg 8.009 r_dihedral_angle_1_deg 6.456 r_lrange_it 5.016 r_lrange_other 4.98 r_scangle_it 3.989 r_scangle_other 3.987 r_scbond_it 2.604 r_scbond_other 2.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.254 r_dihedral_angle_3_deg 11.915 r_dihedral_angle_2_deg 8.009 r_dihedral_angle_1_deg 6.456 r_lrange_it 5.016 r_lrange_other 4.98 r_scangle_it 3.989 r_scangle_other 3.987 r_scbond_it 2.604 r_scbond_other 2.602 r_angle_refined_deg 1.929 r_mcangle_other 1.928 r_mcangle_it 1.927 r_mcbond_it 1.297 r_mcbond_other 1.281 r_angle_other_deg 0.69 r_xyhbond_nbd_refined 0.333 r_nbd_refined 0.256 r_symmetry_nbd_other 0.202 r_symmetry_nbd_refined 0.194 r_nbtor_refined 0.185 r_nbd_other 0.178 r_symmetry_xyhbond_nbd_refined 0.125 r_chiral_restr 0.101 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.039 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 87 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement