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Crystal structure of hen egg white lysozyme at 100 Kelvin with Apiezon N (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 sodium chloride, 100 mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2 38.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.313 α = 90 b = 78.313 β = 90 c = 37.382 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 2023-11-01 M SINGLE WAVELENGTH
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 1.496 25.558 99.33 0.8797 17.53 10 19312
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 24.61 0.8797
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.496 25.558 19285 951 99.757 0.217 0.2158 0.2243 0.2492 0.2562 10.71
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] 0.003 0.003 -0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.29 r_dihedral_angle_6_deg 15.496 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_1_deg 6.489 r_lrange_it 3.927 r_lrange_other 3.883 r_scangle_it 3.091 r_scangle_other 3.089 r_scbond_it 2.053 r_scbond_other 2.051
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.29 r_dihedral_angle_6_deg 15.496 r_dihedral_angle_3_deg 12.562 r_dihedral_angle_1_deg 6.489 r_lrange_it 3.927 r_lrange_other 3.883 r_scangle_it 3.091 r_scangle_other 3.089 r_scbond_it 2.053 r_scbond_other 2.051 r_angle_refined_deg 1.85 r_mcangle_other 1.519 r_mcangle_it 1.509 r_mcbond_it 0.993 r_mcbond_other 0.992 r_angle_other_deg 0.667 r_xyhbond_nbd_refined 0.375 r_nbd_refined 0.265 r_symmetry_nbd_other 0.203 r_nbtor_refined 0.183 r_symmetry_xyhbond_nbd_refined 0.183 r_nbd_other 0.142 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.082 r_symmetry_nbd_refined 0.065 r_metal_ion_refined 0.014 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 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 90 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement