☰ Navigation Tabs
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 = 77.416 α = 90 b = 77.416 β = 90 c = 37.219 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 2021-01-15 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 13.41 99 0.125 0.14 0.06 0.934 7 4.9 15278
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 97.3 1.352 1.609 0.859 0.387 3.1
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 13.41 14503 747 98.51 0.24168 0.23947 0.2476 0.28684 0.294 RANDOM 17.707
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] 0.5 0.5 -0.99
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.116 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 6.86 r_long_range_B_refined 5.212 r_long_range_B_other 4.825 r_scangle_other 2.686 r_mcangle_it 1.901 r_mcangle_other 1.9 r_scbond_it 1.713
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.116 r_dihedral_angle_4_deg 14.586 r_dihedral_angle_3_deg 13.192 r_dihedral_angle_1_deg 6.86 r_long_range_B_refined 5.212 r_long_range_B_other 4.825 r_scangle_other 2.686 r_mcangle_it 1.901 r_mcangle_other 1.9 r_scbond_it 1.713 r_scbond_other 1.711 r_angle_refined_deg 1.545 r_angle_other_deg 1.429 r_mcbond_it 1.221 r_mcbond_other 1.221 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 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 170 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction MOLREP phasing