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Crystal structure of hen egg white lysozyme at 275 Kelvin (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 2.09 41.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.738 α = 90 b = 79.738 β = 90 c = 37.699 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 275 CMOS BRUKER PHOTON 100 2020-11-04 L LAUE
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 1.5 22.59 99.78 0.802 7.62 1.9 20065
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 1.5 22.59 0.802
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 3A8Z 1.5 22.587 20065 1032 99.776 0.172 0.171 0.1796 0.1902 0.2021 16.981
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 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.793 r_dihedral_angle_4_deg 20.247 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 6.571 r_lrange_it 6.161 r_lrange_other 6.161 r_scangle_it 5.042 r_scangle_other 5.039 r_scbond_it 3.263 r_scbond_other 3.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.793 r_dihedral_angle_4_deg 20.247 r_dihedral_angle_3_deg 13.28 r_dihedral_angle_1_deg 6.571 r_lrange_it 6.161 r_lrange_other 6.161 r_scangle_it 5.042 r_scangle_other 5.039 r_scbond_it 3.263 r_scbond_other 3.26 r_mcangle_other 2.243 r_mcangle_it 2.24 r_angle_refined_deg 1.784 r_angle_other_deg 1.603 r_mcbond_it 1.514 r_mcbond_other 1.5 r_symmetry_nbd_refined 0.46 r_nbd_other 0.265 r_nbd_refined 0.239 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.176 r_symmetry_xyhbond_nbd_refined 0.167 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.094 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.04 r_bond_refined_d 0.013 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 51 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction