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Crystal structure of hen egg white lysozyme at 300 Kelvin with Vaseline (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 41.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.891 α = 90 b = 78.891 β = 90 c = 38.526 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 1.497 26.019 99 0.99 18 1 19892
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 1.497 26.019 19892 973 98.583 0.184 0.1825 0.1826 0.2084 0.2069 18.605
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 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.339 r_dihedral_angle_3_deg 11.595 r_dihedral_angle_2_deg 10.818 r_lrange_it 6.941 r_lrange_other 6.939 r_dihedral_angle_1_deg 6.585 r_scangle_it 5.77 r_scangle_other 5.766 r_scbond_it 3.691 r_scbond_other 3.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.339 r_dihedral_angle_3_deg 11.595 r_dihedral_angle_2_deg 10.818 r_lrange_it 6.941 r_lrange_other 6.939 r_dihedral_angle_1_deg 6.585 r_scangle_it 5.77 r_scangle_other 5.766 r_scbond_it 3.691 r_scbond_other 3.688 r_mcangle_other 2.678 r_mcangle_it 2.667 r_angle_refined_deg 2.01 r_mcbond_it 1.792 r_mcbond_other 1.788 r_angle_other_deg 0.713 r_xyhbond_nbd_refined 0.477 r_nbd_refined 0.257 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.182 r_chiral_restr 0.12 r_nbd_other 0.119 r_symmetry_nbtor_other 0.08 r_symmetry_xyhbond_nbd_refined 0.055 r_metal_ion_refined 0.035 r_bond_refined_d 0.011 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 51 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement