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Crystal structure of hen egg white lysozyme at 250 Kelvin
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 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.318 α = 90 b = 79.318 β = 90 c = 37.756 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 250 CMOS BRUKER PHOTON 100 2020-11-04 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 25.1 99.66 0.758 8.34 1.9 19866
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 25.1 0.758
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 25.095 19866 1014 99.664 0.166 0.1644 0.1738 0.1909 0.2042 15.127
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 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.185 r_dihedral_angle_3_deg 13.543 r_dihedral_angle_4_deg 12.994 r_dihedral_angle_1_deg 6.667 r_lrange_it 5.845 r_lrange_other 5.834 r_scangle_it 4.466 r_scangle_other 4.463 r_scbond_it 2.882 r_scbond_other 2.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.185 r_dihedral_angle_3_deg 13.543 r_dihedral_angle_4_deg 12.994 r_dihedral_angle_1_deg 6.667 r_lrange_it 5.845 r_lrange_other 5.834 r_scangle_it 4.466 r_scangle_other 4.463 r_scbond_it 2.882 r_scbond_other 2.88 r_mcangle_other 2.068 r_mcangle_it 2.064 r_angle_refined_deg 1.82 r_angle_other_deg 1.624 r_mcbond_it 1.355 r_mcbond_other 1.333 r_nbd_refined 0.234 r_symmetry_nbd_other 0.197 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.138 r_nbd_other 0.12 r_chiral_restr 0.099 r_symmetry_nbd_refined 0.098 r_symmetry_nbtor_other 0.085 r_metal_ion_refined 0.074 r_symmetry_xyhbond_nbd_refined 0.057 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction