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Crystal structure of hen egg white lysozyme at 100 Kelvin with Apiezon N (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 295 1.2 M sodium chloride, 100 mM sodium acetate, pH 4.6
Crystal Properties Matthews coefficient Solvent content 2 38.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.345 α = 90 b = 78.345 β = 90 c = 37.269 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 PIXEL Bruker PHOTON II 2024-07-01 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 1.499 27.001 99 0.9 16 20 19135
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 10 0.99
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 1.499 27.001 19135 941 99.755 0.207 0.206 0.2132 0.2361 0.243 8.78
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] -0.011 -0.011 0.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.316 r_dihedral_angle_3_deg 11.874 r_dihedral_angle_2_deg 7.169 r_dihedral_angle_1_deg 6.553 r_lrange_it 3.726 r_lrange_other 3.641 r_scangle_it 2.838 r_scangle_other 2.836 r_angle_refined_deg 1.854 r_scbond_it 1.814
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.316 r_dihedral_angle_3_deg 11.874 r_dihedral_angle_2_deg 7.169 r_dihedral_angle_1_deg 6.553 r_lrange_it 3.726 r_lrange_other 3.641 r_scangle_it 2.838 r_scangle_other 2.836 r_angle_refined_deg 1.854 r_scbond_it 1.814 r_scbond_other 1.813 r_mcangle_other 1.377 r_mcangle_it 1.375 r_mcbond_it 0.894 r_mcbond_other 0.889 r_angle_other_deg 0.654 r_xyhbond_nbd_refined 0.388 r_symmetry_xyhbond_nbd_refined 0.329 r_nbd_refined 0.265 r_symmetry_nbd_other 0.202 r_nbtor_refined 0.184 r_nbd_other 0.13 r_chiral_restr 0.097 r_symmetry_nbtor_other 0.078 r_metal_ion_refined 0.071 r_symmetry_nbd_refined 0.05 r_bond_refined_d 0.009 r_gen_planes_refined 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 86 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement SAINT data reduction