☰ Navigation Tabs
Crystal structure of hen egg white lysozyme at 100 Kelvin with Silicone Oil (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 38.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.505 α = 90 b = 78.505 β = 90 c = 37.123 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 1.498 21.773 99 0.99 18 1 19158
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 1.498 21.773 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 1.498 21.773 19158 945 99.703 0.178 0.1764 0.1767 0.2087 0.2086 10.572
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] -0.001 -0.001 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.615 r_dihedral_angle_3_deg 13.725 r_dihedral_angle_2_deg 11.884 r_dihedral_angle_1_deg 6.394 r_lrange_it 4.292 r_lrange_other 4.099 r_scangle_it 2.985 r_scangle_other 2.983 r_scbond_it 2.304 r_scbond_other 2.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 17.615 r_dihedral_angle_3_deg 13.725 r_dihedral_angle_2_deg 11.884 r_dihedral_angle_1_deg 6.394 r_lrange_it 4.292 r_lrange_other 4.099 r_scangle_it 2.985 r_scangle_other 2.983 r_scbond_it 2.304 r_scbond_other 2.302 r_angle_refined_deg 1.841 r_mcangle_it 1.529 r_mcangle_other 1.528 r_mcbond_it 1.05 r_mcbond_other 1.035 r_angle_other_deg 0.626 r_xyhbond_nbd_refined 0.296 r_nbd_refined 0.252 r_symmetry_nbd_other 0.205 r_nbtor_refined 0.181 r_nbd_other 0.155 r_symmetry_xyhbond_nbd_refined 0.147 r_chiral_restr 0.091 r_symmetry_nbtor_other 0.083 r_metal_ion_refined 0.075 r_symmetry_nbd_refined 0.039 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