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Crystal structure of hen egg white lysozyme at 100 Kelvin with PEG 6000 (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 NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 1.99 38.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.416 α = 90 b = 78.416 β = 90 c = 37.171 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 22.224 99 0.99 18 1 19112
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 22.224 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 1.499 22.224 19112 943 99.802 0.176 0.1742 0.1828 0.2052 0.2141 9.725
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] -0.003 -0.003 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.827 r_dihedral_angle_6_deg 18.252 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_1_deg 6.511 r_lrange_it 4.137 r_lrange_other 3.886 r_scangle_it 2.911 r_scangle_other 2.909 r_scbond_it 2.219 r_scbond_other 2.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 20.827 r_dihedral_angle_6_deg 18.252 r_dihedral_angle_3_deg 13.054 r_dihedral_angle_1_deg 6.511 r_lrange_it 4.137 r_lrange_other 3.886 r_scangle_it 2.911 r_scangle_other 2.909 r_scbond_it 2.219 r_scbond_other 2.216 r_angle_refined_deg 1.847 r_mcangle_it 1.368 r_mcangle_other 1.367 r_mcbond_it 0.902 r_mcbond_other 0.9 r_angle_other_deg 0.638 r_xyhbond_nbd_refined 0.314 r_nbd_refined 0.261 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.183 r_nbd_other 0.172 r_symmetry_xyhbond_nbd_refined 0.136 r_chiral_restr 0.088 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.068 r_symmetry_nbd_refined 0.026 r_gen_planes_refined 0.011 r_bond_refined_d 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 169 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement