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Crystal structure of hen egg white lysozyme at 175 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 2.01 38.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.776 α = 90 b = 78.776 β = 90 c = 37.16 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 24.92 99.66 0.793 6.31 1.9 19272
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 24.92 0.793
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 24.92 19272 986 99.664 0.187 0.1855 0.1947 0.2226 0.2311 13.488
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 30.938 r_dihedral_angle_4_deg 21.358 r_dihedral_angle_3_deg 14.197 r_dihedral_angle_1_deg 6.936 r_lrange_it 4.154 r_lrange_other 4.133 r_scangle_it 3.298 r_scangle_other 3.296 r_scbond_it 2.253 r_scbond_other 2.251
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.938 r_dihedral_angle_4_deg 21.358 r_dihedral_angle_3_deg 14.197 r_dihedral_angle_1_deg 6.936 r_lrange_it 4.154 r_lrange_other 4.133 r_scangle_it 3.298 r_scangle_other 3.296 r_scbond_it 2.253 r_scbond_other 2.251 r_mcangle_other 1.848 r_mcangle_it 1.846 r_angle_refined_deg 1.716 r_angle_other_deg 1.571 r_mcbond_it 1.266 r_mcbond_other 1.19 r_nbd_refined 0.239 r_symmetry_nbd_other 0.191 r_nbd_other 0.182 r_nbtor_refined 0.171 r_xyhbond_nbd_refined 0.12 r_symmetry_xyhbond_nbd_other 0.095 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.085 r_symmetry_nbd_refined 0.075 r_symmetry_xyhbond_nbd_refined 0.069 r_metal_ion_refined 0.065 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 102 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction