☰ 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 = 77.357 α = 90 b = 77.357 β = 90 c = 37.164 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 2021-01-14 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 14.05 99.1 0.277 0.314 0.141 0.93 7.5 4.7 15248
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 99.6 5.957 7.201 3.971 0.159 2.9
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 14.05 14471 746 98.64 0.22421 0.22215 0.2294 0.26518 0.2696 RANDOM 17.426
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] 0.35 0.35 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.088 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 14.052 r_dihedral_angle_1_deg 7.037 r_long_range_B_refined 5.204 r_long_range_B_other 4.958 r_scangle_other 3.676 r_scbond_it 2.416 r_scbond_other 2.414 r_mcangle_it 2.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.088 r_dihedral_angle_4_deg 14.491 r_dihedral_angle_3_deg 14.052 r_dihedral_angle_1_deg 7.037 r_long_range_B_refined 5.204 r_long_range_B_other 4.958 r_scangle_other 3.676 r_scbond_it 2.416 r_scbond_other 2.414 r_mcangle_it 2.261 r_mcangle_other 2.26 r_angle_refined_deg 1.676 r_angle_other_deg 1.482 r_mcbond_it 1.418 r_mcbond_other 1.417 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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 131 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement Aimless data scaling HKL-2000 data reduction MOLREP phasing