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Crystal structure of hen egg white lysozyme at 300 Kelvin with Vaseline (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 295 1.2 M NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 2.08 40.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.226 α = 90 b = 79.226 β = 90 c = 38.047 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 28.011 99 0.99 18 1 19887
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 28.011 19887 969 99.37 0.202 0.2006 0.2089 0.2358 0.2379 16.509
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_6_deg 15.149 r_dihedral_angle_3_deg 12.216 r_dihedral_angle_2_deg 7.755 r_dihedral_angle_1_deg 6.633 r_lrange_it 6.299 r_lrange_other 6.293 r_scangle_it 4.84 r_scangle_other 4.836 r_scbond_it 2.986 r_scbond_other 2.983
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.149 r_dihedral_angle_3_deg 12.216 r_dihedral_angle_2_deg 7.755 r_dihedral_angle_1_deg 6.633 r_lrange_it 6.299 r_lrange_other 6.293 r_scangle_it 4.84 r_scangle_other 4.836 r_scbond_it 2.986 r_scbond_other 2.983 r_mcangle_other 2.41 r_mcangle_it 2.402 r_angle_refined_deg 1.761 r_mcbond_it 1.553 r_mcbond_other 1.549 r_angle_other_deg 0.648 r_xyhbond_nbd_refined 0.416 r_nbd_refined 0.248 r_symmetry_nbd_other 0.2 r_nbtor_refined 0.18 r_metal_ion_refined 0.158 r_nbd_other 0.13 r_chiral_restr 0.103 r_symmetry_xyhbond_nbd_refined 0.097 r_symmetry_nbtor_other 0.078 r_gen_planes_refined 0.009 r_symmetry_nbd_refined 0.009 r_bond_refined_d 0.008 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 56 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement