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Crystal structure of hen egg white lysozyme at 300 Kelvin with Apiezon T
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 2.08 40.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.098 α = 90 b = 79.098 β = 90 c = 38.129 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 300 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 1.468 27.45 99 0.99 18 1 20433
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 1.468 27.45 20433 1003 96.337 0.179 0.1764 0.1764 0.2341 0.2343 19.924
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] -0.009 -0.009 0.017
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.658 r_lrange_other 22.621 r_dihedral_angle_6_deg 14.42 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_2_deg 8.895 r_dihedral_angle_1_deg 6.231 r_scangle_it 5.749 r_scangle_other 5.746 r_scbond_it 3.692 r_scbond_other 3.688
RMS Deviations Key Refinement Restraint Deviation r_lrange_it 22.658 r_lrange_other 22.621 r_dihedral_angle_6_deg 14.42 r_dihedral_angle_3_deg 11.52 r_dihedral_angle_2_deg 8.895 r_dihedral_angle_1_deg 6.231 r_scangle_it 5.749 r_scangle_other 5.746 r_scbond_it 3.692 r_scbond_other 3.688 r_mcangle_other 2.776 r_mcangle_it 2.76 r_angle_refined_deg 1.908 r_mcbond_it 1.849 r_mcbond_other 1.848 r_angle_other_deg 0.67 r_xyhbond_nbd_refined 0.417 r_nbd_refined 0.359 r_symmetry_nbd_other 0.293 r_symmetry_xyhbond_nbd_refined 0.258 r_nbd_other 0.236 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.177 r_chiral_restr 0.103 r_symmetry_nbtor_other 0.08 r_metal_ion_refined 0.05 r_symmetry_xyhbond_nbd_other 0.027 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement