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Crystal structure of hen egg white lysozyme at 300 Kelvin with Apiezon T (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 2.07 40.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.902 α = 90 b = 78.902 β = 90 c = 38.145 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 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 25.903 99 0.99 18 1 19830
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 25.903 19830 967 99.583 0.249 0.247 0.2517 0.2825 0.2823 16.316
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] -0.027 -0.027 0.053
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.792 r_dihedral_angle_3_deg 11.478 r_dihedral_angle_2_deg 6.98 r_dihedral_angle_1_deg 6.758 r_lrange_it 5.916 r_lrange_other 5.915 r_scangle_it 4.518 r_scangle_other 4.515 r_scbond_it 2.817 r_scbond_other 2.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.792 r_dihedral_angle_3_deg 11.478 r_dihedral_angle_2_deg 6.98 r_dihedral_angle_1_deg 6.758 r_lrange_it 5.916 r_lrange_other 5.915 r_scangle_it 4.518 r_scangle_other 4.515 r_scbond_it 2.817 r_scbond_other 2.814 r_mcangle_other 2.204 r_mcangle_it 2.203 r_angle_refined_deg 1.647 r_mcbond_it 1.447 r_mcbond_other 1.41 r_angle_other_deg 0.595 r_xyhbond_nbd_refined 0.448 r_nbd_refined 0.248 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.182 r_metal_ion_refined 0.142 r_symmetry_xyhbond_nbd_refined 0.124 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.078 r_nbd_other 0.074 r_symmetry_nbd_refined 0.026 r_gen_planes_refined 0.008 r_bond_refined_d 0.007 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 46 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement