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Crystal structure of hen egg white lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 EVAPORATION 4.6 295 1.2 M NaCl, 100 mM Sodium Acetate, 50 mg/mL Lyzozyme, 30% Glycerol for cryoprotection
Crystal Properties Matthews coefficient Solvent content 1.99 37.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.38 α = 90 b = 78.38 β = 90 c = 36.934 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 125 CCD OXFORD TITAN CCD 2020-08-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.54056
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.6 14.07 99.5 0.05 0.056 0.024 0.998 16.2 4.7 15627
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.63 98.2 0.352 0.428 0.239 0.863 3
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 14.08 14806 793 99.31 0.19516 0.19383 0.2042 0.2189 0.226 RANDOM 13.012
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] 0.14 0.14 -0.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.917 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 11.723 r_dihedral_angle_1_deg 6.745 r_long_range_B_refined 4.601 r_long_range_B_other 4.465 r_scangle_other 3.051 r_scbond_it 2.054 r_scbond_other 2.052 r_angle_refined_deg 1.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.917 r_dihedral_angle_4_deg 15.969 r_dihedral_angle_3_deg 11.723 r_dihedral_angle_1_deg 6.745 r_long_range_B_refined 4.601 r_long_range_B_other 4.465 r_scangle_other 3.051 r_scbond_it 2.054 r_scbond_other 2.052 r_angle_refined_deg 1.751 r_angle_other_deg 1.659 r_mcangle_other 1.507 r_mcangle_it 1.505 r_mcbond_it 1.023 r_mcbond_other 1.017 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1000 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction PDB_EXTRACT data extraction