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Crystal structure of hen egg white lysozyme at 300 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 2.08 40.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.495 α = 90 b = 79.495 β = 90 c = 37.767 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 300 CMOS BRUKER PHOTON 100 2020-11-24 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 56.21 99.58 0.806 8.77 1.9 20015
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 56.21 0.806
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 56.21 20015 1032 99.582 0.176 0.1746 0.1744 0.1959 0.1961 22.015
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 32.046 r_dihedral_angle_4_deg 17.936 r_dihedral_angle_3_deg 13.298 r_lrange_it 7.485 r_lrange_other 7.484 r_dihedral_angle_1_deg 6.645 r_scangle_it 6.077 r_scangle_other 6.073 r_scbond_it 3.923 r_scbond_other 3.919
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.046 r_dihedral_angle_4_deg 17.936 r_dihedral_angle_3_deg 13.298 r_lrange_it 7.485 r_lrange_other 7.484 r_dihedral_angle_1_deg 6.645 r_scangle_it 6.077 r_scangle_other 6.073 r_scbond_it 3.923 r_scbond_other 3.919 r_mcangle_it 2.912 r_mcangle_other 2.912 r_mcbond_it 1.971 r_mcbond_other 1.938 r_angle_refined_deg 1.829 r_angle_other_deg 1.615 r_nbd_refined 0.235 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.175 r_symmetry_xyhbond_nbd_refined 0.118 r_nbd_other 0.117 r_xyhbond_nbd_refined 0.115 r_chiral_restr 0.105 r_metal_ion_refined 0.094 r_symmetry_nbtor_other 0.089 r_symmetry_nbd_refined 0.02 r_bond_refined_d 0.013 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 42 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction