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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 = 77.821 α = 90 b = 77.821 β = 90 c = 37.311 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 2021-02-24 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 14.11 99.4 0.174 0.197 0.087 0.815 4.7 4.7 15554
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 97.8 2.204 2.674 1.477 0.151 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.6 14.12 14730 789 99.16 0.2468 0.24419 0.29442 0.2989 RANDOM 22.246
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] 0.56 0.56 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.564 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_4_deg 10.982 r_dihedral_angle_1_deg 7.394 r_long_range_B_refined 6.307 r_long_range_B_other 6.252 r_scangle_other 3.964 r_mcangle_it 2.764 r_mcangle_other 2.764 r_scbond_it 2.547
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.564 r_dihedral_angle_3_deg 16.151 r_dihedral_angle_4_deg 10.982 r_dihedral_angle_1_deg 7.394 r_long_range_B_refined 6.307 r_long_range_B_other 6.252 r_scangle_other 3.964 r_mcangle_it 2.764 r_mcangle_other 2.764 r_scbond_it 2.547 r_scbond_other 2.544 r_mcbond_it 1.848 r_mcbond_other 1.846 r_angle_refined_deg 1.686 r_angle_other_deg 1.449 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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 146 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction MOLREP phasing