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Crystal structure of hen egg white lysozyme at 100 Kelvin with PEG 6000 (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 38.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.507 α = 90 b = 78.507 β = 90 c = 37.15 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 22.236 99 0.99 18 1 19145
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 1.499 22.236 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 22.236 19145 943 99.771 0.176 0.1743 0.1835 0.2036 0.2123 10.33
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 22.733 r_dihedral_angle_6_deg 17.456 r_dihedral_angle_3_deg 13.571 r_dihedral_angle_1_deg 6.482 r_lrange_it 4.79 r_lrange_other 4.591 r_scangle_it 3.093 r_scangle_other 3.091 r_scbond_it 2.39 r_scbond_other 2.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 22.733 r_dihedral_angle_6_deg 17.456 r_dihedral_angle_3_deg 13.571 r_dihedral_angle_1_deg 6.482 r_lrange_it 4.79 r_lrange_other 4.591 r_scangle_it 3.093 r_scangle_other 3.091 r_scbond_it 2.39 r_scbond_other 2.388 r_angle_refined_deg 1.821 r_mcangle_it 1.456 r_mcangle_other 1.455 r_mcbond_it 0.977 r_mcbond_other 0.967 r_angle_other_deg 0.636 r_xyhbond_nbd_refined 0.309 r_nbd_refined 0.253 r_symmetry_nbd_other 0.205 r_symmetry_xyhbond_nbd_refined 0.198 r_nbtor_refined 0.182 r_nbd_other 0.174 r_metal_ion_refined 0.101 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.081 r_symmetry_nbd_refined 0.037 r_gen_planes_refined 0.011 r_bond_refined_d 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 158 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement