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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 PDB 6QWY
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 1.97 37.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.247 α = 90 b = 78.247 β = 90 c = 36.948 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 CMOS BRUKER PHOTON 100 2020-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE BRUKER IMUS 3.0 MICROFOCUS 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.596 25.42 99.67 0.108 10.12 9.88 15713
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.596 1.653 0.312
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 6qwy 1.6 25.42 14904 800 99.73 0.182 0.18 0.1885 0.2176 0.2214 RANDOM 11.85
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] 0.15 0.15 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.307 r_dihedral_angle_4_deg 14.13 r_dihedral_angle_3_deg 12.263 r_dihedral_angle_1_deg 6.725 r_angle_refined_deg 1.714 r_angle_other_deg 1.614 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.307 r_dihedral_angle_4_deg 14.13 r_dihedral_angle_3_deg 12.263 r_dihedral_angle_1_deg 6.725 r_angle_refined_deg 1.714 r_angle_other_deg 1.614 r_chiral_restr 0.095 r_bond_refined_d 0.011 r_gen_planes_refined 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 1000 Nucleic Acid Atoms Solvent Atoms 154 Heterogen Atoms 1
Software Software Software Name Purpose XDS data reduction SAINT data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction