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Crystal structure of hen egg white lysozyme at 100 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 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.679 α = 90 b = 78.679 β = 90 c = 37.111 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 100 CMOS BRUKER PHOTON 100 2020-10-05 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 1.498 22.27 99.79 0.805 7.9 1.9 19250
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 22.27 0.805
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 1.498 22.268 19250 986 99.793 0.178 0.1761 0.1844 0.2121 0.2176 10.963
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 31.012 r_dihedral_angle_4_deg 16.467 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_1_deg 6.768 r_lrange_it 3.886 r_lrange_other 3.814 r_scangle_it 2.901 r_scangle_other 2.899 r_scbond_it 1.975 r_scbond_other 1.973
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.012 r_dihedral_angle_4_deg 16.467 r_dihedral_angle_3_deg 13.227 r_dihedral_angle_1_deg 6.768 r_lrange_it 3.886 r_lrange_other 3.814 r_scangle_it 2.901 r_scangle_other 2.899 r_scbond_it 1.975 r_scbond_other 1.973 r_angle_refined_deg 1.867 r_angle_other_deg 1.634 r_mcangle_it 1.549 r_mcangle_other 1.549 r_mcbond_it 1.054 r_mcbond_other 1.006 r_nbd_refined 0.246 r_symmetry_nbd_other 0.191 r_nbtor_refined 0.174 r_symmetry_xyhbond_nbd_refined 0.163 r_nbd_other 0.155 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.086 r_metal_ion_refined 0.084 r_symmetry_nbd_refined 0.076 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_xyhbond_nbd_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction