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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 193L PDB ENTRY 193L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.5 293 sodium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.785 α = 90 b = 78.785 β = 90 c = 36.961 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 100 IMAGE PLATE RIGAKU RAXIS VII 2008-11-17 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) R Merge I (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 1.4 80 98 0.05 20.1 23090 16.973
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.4 1.45 84.8 0.172 6.9
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 PDB ENTRY 193L 1.4 16.73 21868 1186 98.16 0.19383 0.19286 0.1868 0.21239 0.2047 RANDOM 15.058
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_1_deg 5.421 r_scangle_it 2.674 r_scbond_it 1.689 r_angle_refined_deg 1.144 r_mcangle_it 1.063 r_mcbond_it 0.549 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.755 r_dihedral_angle_4_deg 17.615 r_dihedral_angle_3_deg 12.232 r_dihedral_angle_1_deg 5.421 r_scangle_it 2.674 r_scbond_it 1.689 r_angle_refined_deg 1.144 r_mcangle_it 1.063 r_mcbond_it 0.549 r_nbtor_refined 0.301 r_nbd_refined 0.211 r_symmetry_hbond_refined 0.165 r_symmetry_vdw_refined 0.16 r_xyhbond_nbd_refined 0.094 r_chiral_restr 0.087 r_metal_ion_refined 0.078 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 20
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling