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High resolution X-ray crystal structure of Tetragonal Hen egg white lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 193L pdb entry 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 4.7 293 0.04N NaOAc/HOAc buffer, pH 4.7, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.341 α = 90 b = 79.341 β = 90 c = 37.867 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 293 IMAGE PLATE RIGAKU M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.62 55.9 98.6 15495 15495 1 1 23.872
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.62 98.6 15495
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 193L 1.62 28.1 1 1 15495 15495 789 98.55 0.23095 0.23095 0.22855 0.2773 0.2504 RANDOM 23.872
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] -0.39 -0.39 0.77
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.65 r_scangle_it 5.972 r_dihedral_angle_1_deg 4.989 r_scbond_it 3.999 r_mcangle_it 2.677 r_angle_refined_deg 2.593 r_mcbond_it 1.951 r_angle_other_deg 1.366 r_symmetry_hbond_refined 0.506 r_symmetry_vdw_other 0.493
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.65 r_scangle_it 5.972 r_dihedral_angle_1_deg 4.989 r_scbond_it 3.999 r_mcangle_it 2.677 r_angle_refined_deg 2.593 r_mcbond_it 1.951 r_angle_other_deg 1.366 r_symmetry_hbond_refined 0.506 r_symmetry_vdw_other 0.493 r_symmetry_vdw_refined 0.453 r_nbd_refined 0.236 r_nbd_other 0.22 r_symmetry_hbond_other 0.207 r_xyhbond_nbd_refined 0.203 r_chiral_restr 0.168 r_bond_refined_d 0.03 r_gen_planes_refined 0.017 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 81 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345 data collection AUTOMAR data reduction AMoRE phasing