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Crystal structure of hen egg white lysozyme at 100 Kelvin with Silicone Oil (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 2 38.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.488 α = 90 b = 78.488 β = 90 c = 37.169 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 21.769 99 0.99 18 1 19152
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 21.769 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 21.769 19152 945 99.823 0.169 0.1674 0.1765 0.1975 0.2063 9.851
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] -0.001 -0.001 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.175 r_dihedral_angle_6_deg 17.846 r_dihedral_angle_3_deg 13.209 r_dihedral_angle_1_deg 6.452 r_lrange_it 4.863 r_lrange_other 4.56 r_scangle_it 3.175 r_scangle_other 3.173 r_scbond_it 2.438 r_scbond_other 2.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 23.175 r_dihedral_angle_6_deg 17.846 r_dihedral_angle_3_deg 13.209 r_dihedral_angle_1_deg 6.452 r_lrange_it 4.863 r_lrange_other 4.56 r_scangle_it 3.175 r_scangle_other 3.173 r_scbond_it 2.438 r_scbond_other 2.436 r_angle_refined_deg 1.843 r_mcangle_other 1.444 r_mcangle_it 1.443 r_mcbond_it 0.955 r_mcbond_other 0.954 r_angle_other_deg 0.631 r_xyhbond_nbd_refined 0.295 r_nbd_refined 0.265 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.182 r_nbd_other 0.161 r_symmetry_xyhbond_nbd_refined 0.132 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.081 r_metal_ion_refined 0.068 r_symmetry_nbd_refined 0.017 r_bond_refined_d 0.011 r_gen_planes_refined 0.011 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 178 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement