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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 1.99 38.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.492 α = 90 b = 77.492 β = 90 c = 37.064 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 2020-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SEALED TUBE OXFORD DIFFRACTION ENHANCE ULTRA 1.5406
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 13.41 98.6 0.098 0.109 0.046 0.997 10.6 4.9 15223
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 91.2 1.442 1.746 0.964 0.406 3.1
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 13.42 14440 746 98.41 0.21054 0.20859 0.2169 0.24972 0.2569 RANDOM 18.458
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] 0.87 0.87 -1.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.353 r_dihedral_angle_4_deg 13.698 r_dihedral_angle_3_deg 12.731 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 4.93 r_long_range_B_other 4.765 r_scangle_other 3.178 r_scbond_it 2.059 r_scbond_other 2.057 r_mcangle_it 2.022
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.353 r_dihedral_angle_4_deg 13.698 r_dihedral_angle_3_deg 12.731 r_dihedral_angle_1_deg 6.878 r_long_range_B_refined 4.93 r_long_range_B_other 4.765 r_scangle_other 3.178 r_scbond_it 2.059 r_scbond_other 2.057 r_mcangle_it 2.022 r_mcangle_other 2.02 r_angle_refined_deg 1.523 r_angle_other_deg 1.458 r_mcbond_it 1.296 r_mcbond_other 1.296 r_chiral_restr 0.073 r_gen_planes_refined 0.009 r_bond_refined_d 0.008 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 132 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction MOLREP phasing