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Crystal structure of hen egg white lysozyme at 300 Kelvin with Vaseline
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 41.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.125 α = 90 b = 79.125 β = 90 c = 38.221 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 1.5 27.975 99 0.99 18 1 19888
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 1.5 27.975 19888 969 99.395 0.196 0.1934 0.2033 0.2438 0.2502 17.568
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] -0.002 -0.002 0.005
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 21.146 r_lrange_it 21.048 r_dihedral_angle_6_deg 15.138 r_dihedral_angle_3_deg 11.748 r_dihedral_angle_2_deg 7.622 r_dihedral_angle_1_deg 6.521 r_scangle_it 4.929 r_scangle_other 4.926 r_scbond_it 3.039 r_scbond_other 3.036
RMS Deviations Key Refinement Restraint Deviation r_lrange_other 21.146 r_lrange_it 21.048 r_dihedral_angle_6_deg 15.138 r_dihedral_angle_3_deg 11.748 r_dihedral_angle_2_deg 7.622 r_dihedral_angle_1_deg 6.521 r_scangle_it 4.929 r_scangle_other 4.926 r_scbond_it 3.039 r_scbond_other 3.036 r_mcangle_other 2.465 r_mcangle_it 2.455 r_angle_refined_deg 1.737 r_mcbond_it 1.588 r_mcbond_other 1.581 r_angle_other_deg 0.637 r_xyhbond_nbd_refined 0.398 r_nbd_refined 0.352 r_symmetry_nbd_other 0.278 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_refined 0.197 r_nbtor_refined 0.18 r_nbd_other 0.12 r_metal_ion_refined 0.105 r_chiral_restr 0.096 r_symmetry_nbtor_other 0.078 r_gen_planes_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 216 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement