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Crystal structure of hen egg white lysozyme at 150 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 38.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.72 α = 90 b = 78.72 β = 90 c = 37.078 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 150 CMOS BRUKER PHOTON 100 2020-10-13 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 24.91 99.85 0.789 7.19 1.91 19259
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 24.91 0.789
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 24.906 19259 986 99.855 0.166 0.1645 0.1742 0.19 0.2005 10.019
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 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.512 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 11.681 r_dihedral_angle_1_deg 6.63 r_lrange_it 4.107 r_lrange_other 3.963 r_scangle_it 3.048 r_scangle_other 3.046 r_scbond_other 2.061 r_scbond_it 2.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.512 r_dihedral_angle_4_deg 18.276 r_dihedral_angle_3_deg 11.681 r_dihedral_angle_1_deg 6.63 r_lrange_it 4.107 r_lrange_other 3.963 r_scangle_it 3.048 r_scangle_other 3.046 r_scbond_other 2.061 r_scbond_it 2.06 r_angle_refined_deg 1.83 r_angle_other_deg 1.617 r_mcangle_other 1.364 r_mcangle_it 1.363 r_mcbond_it 0.877 r_mcbond_other 0.858 r_symmetry_nbd_refined 0.275 r_nbd_refined 0.242 r_symmetry_xyhbond_nbd_refined 0.214 r_symmetry_nbd_other 0.197 r_nbd_other 0.196 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.14 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.066 r_xyhbond_nbd_other 0.042 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 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 126 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction