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Crystal structure of hen egg white lysozyme at 175 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 2.01 38.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.753 α = 90 b = 78.753 β = 90 c = 37.11 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 175 CMOS BRUKER PHOTON 100 2020-11-03 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 22.28 99.69 0.841 9.31 1.9 19316
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 22.28 0.841
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 22.28 19316 988 99.685 0.189 0.1869 0.1948 0.2195 0.2248 12.317
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_2_deg 31.638 r_dihedral_angle_4_deg 20.119 r_dihedral_angle_3_deg 13.687 r_dihedral_angle_1_deg 7.097 r_lrange_it 3.865 r_lrange_other 3.858 r_scangle_it 2.978 r_scangle_other 2.976 r_scbond_it 2.074 r_scbond_other 2.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.638 r_dihedral_angle_4_deg 20.119 r_dihedral_angle_3_deg 13.687 r_dihedral_angle_1_deg 7.097 r_lrange_it 3.865 r_lrange_other 3.858 r_scangle_it 2.978 r_scangle_other 2.976 r_scbond_it 2.074 r_scbond_other 2.073 r_angle_refined_deg 1.882 r_mcangle_it 1.709 r_mcangle_other 1.708 r_angle_other_deg 1.609 r_mcbond_it 1.222 r_mcbond_other 1.168 r_nbd_refined 0.238 r_symmetry_nbd_other 0.201 r_nbd_other 0.178 r_nbtor_refined 0.175 r_symmetry_nbd_refined 0.118 r_xyhbond_nbd_refined 0.114 r_symmetry_nbtor_other 0.093 r_chiral_restr 0.091 r_metal_ion_refined 0.089 r_symmetry_xyhbond_nbd_refined 0.076 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 99 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction