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Crystal structure of hen egg white lysozyme at 300 Kelvin with Apiezon N
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 40.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.135 α = 90 b = 79.135 β = 90 c = 38.091 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 1.497 25.025 99 0.99 18 1 19730
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 1.497 25.025 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 1.497 25.025 19730 955 98.355 0.268 0.2664 0.273 0.3092 0.3079 18.257
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] 0.02 0.02 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.949 r_dihedral_angle_3_deg 11.749 r_dihedral_angle_2_deg 7.412 r_dihedral_angle_1_deg 6.859 r_lrange_it 5.06 r_lrange_other 5.05 r_scangle_it 4.071 r_scangle_other 4.068 r_scbond_it 2.627 r_scbond_other 2.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.949 r_dihedral_angle_3_deg 11.749 r_dihedral_angle_2_deg 7.412 r_dihedral_angle_1_deg 6.859 r_lrange_it 5.06 r_lrange_other 5.05 r_scangle_it 4.071 r_scangle_other 4.068 r_scbond_it 2.627 r_scbond_other 2.625 r_mcangle_other 2.466 r_mcangle_it 2.456 r_angle_refined_deg 1.713 r_mcbond_it 1.635 r_mcbond_other 1.623 r_angle_other_deg 0.621 r_xyhbond_nbd_refined 0.526 r_nbd_refined 0.257 r_symmetry_nbd_other 0.204 r_nbtor_refined 0.183 r_nbd_other 0.119 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_refined 0.071 r_metal_ion_refined 0.064 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 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 41 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement