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Crystal structure of hen egg white lysozyme at 125 Kelvin (Duplicate)
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 38.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.782 α = 90 b = 78.782 β = 90 c = 37.17 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 125 CMOS BRUKER PHOTON 100 2020-10-07 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 22.27 99.71 0.765 6.94 1.91 19280
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 0.765
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 22.27 19280 987 99.613 0.187 0.1854 0.1931 0.214 0.2196 10.869
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] -0.006 -0.006 0.012
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.444 r_dihedral_angle_4_deg 20.8 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_1_deg 6.912 r_lrange_it 3.814 r_lrange_other 3.754 r_scangle_it 2.747 r_scangle_other 2.745 r_scbond_it 1.887 r_scbond_other 1.886
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.444 r_dihedral_angle_4_deg 20.8 r_dihedral_angle_3_deg 12.979 r_dihedral_angle_1_deg 6.912 r_lrange_it 3.814 r_lrange_other 3.754 r_scangle_it 2.747 r_scangle_other 2.745 r_scbond_it 1.887 r_scbond_other 1.886 r_angle_refined_deg 1.811 r_angle_other_deg 1.623 r_mcangle_it 1.538 r_mcangle_other 1.537 r_mcbond_it 1.043 r_mcbond_other 0.983 r_nbd_refined 0.238 r_symmetry_nbd_other 0.196 r_nbtor_refined 0.174 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.121 r_symmetry_nbd_refined 0.109 r_chiral_restr 0.092 r_symmetry_nbtor_other 0.087 r_metal_ion_refined 0.086 r_symmetry_xyhbond_nbd_refined 0.075 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 111 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction