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Structure of Hen Egg-White Lysozyme Determined from crystals grown in pH 7.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In-house structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Microbatch, Douglas Instrument robot 7.5 293 0.1 M HEPES-Na pH 7.5, 0.8M Potassium Sodium Tartrate tetrahydrate, Microbatch, Douglas Instrument robot, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.85 33.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.861 α = 90 b = 76.861 β = 90 c = 35.867 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 100 CCD ADSC QUANTUM 210 Mirrors 2005-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.9737 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.201 54.31 98.2 0.054 0.054 16.8 6.2 33587 33587 -3 10.95
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.201 1.22 74.3 0.475 0.419 2.1 2.7 1242
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT In-house structure 1.201 54.31 -3 33538 33538 1688 98.38 0.138 0.138 0.137 0.1369 0.173 0.1706 RANDOM 11.052
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] -1.12 -1.12 2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.808 r_dihedral_angle_4_deg 23.904 r_sphericity_free 14.246 r_dihedral_angle_3_deg 11.511 r_sphericity_bonded 8.756 r_scangle_it 6.77 r_dihedral_angle_1_deg 5.976 r_scbond_it 5.48 r_mcangle_it 4.055 r_mcbond_other 3.411
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.808 r_dihedral_angle_4_deg 23.904 r_sphericity_free 14.246 r_dihedral_angle_3_deg 11.511 r_sphericity_bonded 8.756 r_scangle_it 6.77 r_dihedral_angle_1_deg 5.976 r_scbond_it 5.48 r_mcangle_it 4.055 r_mcbond_other 3.411 r_mcbond_it 3.298 r_rigid_bond_restr 3.015 r_angle_refined_deg 1.697 r_angle_other_deg 1.185 r_symmetry_vdw_other 0.291 r_xyhbond_nbd_refined 0.263 r_nbd_refined 0.25 r_symmetry_hbond_refined 0.218 r_nbd_other 0.215 r_symmetry_vdw_refined 0.188 r_nbtor_refined 0.185 r_chiral_restr 0.11 r_nbtor_other 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1069 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling REFMAC phasing