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Parent Structure of Hen Egg White Lysozyme grown in acidic pH 4.8. Refinement for comparison with crosslinked molecules of lysozyme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In-house model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 293 0.1M Na Acetate, pH 4.8, 7% NaCl, 25% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2 38.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.87 α = 90 b = 78.87 β = 90 c = 36.788 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 2005-06-15 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 1.3 55.73 100 0.057 0.057 10.5 27 29161 29161 -3 10.43
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 1.3 1.32 100 0.538 0.52 3.92 15.9 1416
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 FOURIER SYNTHESIS THROUGHOUT In-house model 1.3 55.73 -3 29111 29111 1477 99.98 0.105 0.105 0.103 0.1045 0.145 0.1429 RANDOM 10.981
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] 0.09 0.09 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.179 r_dihedral_angle_4_deg 19.117 r_sphericity_free 17.031 r_dihedral_angle_3_deg 11.707 r_scangle_it 8.325 r_sphericity_bonded 7.057 r_scbond_it 6.984 r_dihedral_angle_1_deg 5.873 r_mcangle_it 4.52 r_mcbond_it 3.603
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.179 r_dihedral_angle_4_deg 19.117 r_sphericity_free 17.031 r_dihedral_angle_3_deg 11.707 r_scangle_it 8.325 r_sphericity_bonded 7.057 r_scbond_it 6.984 r_dihedral_angle_1_deg 5.873 r_mcangle_it 4.52 r_mcbond_it 3.603 r_rigid_bond_restr 3.475 r_mcbond_other 2.723 r_angle_refined_deg 1.571 r_angle_other_deg 1.141 r_symmetry_vdw_other 0.363 r_nbd_refined 0.268 r_symmetry_vdw_refined 0.256 r_nbd_other 0.23 r_xyhbond_nbd_refined 0.214 r_metal_ion_refined 0.206 r_symmetry_hbond_refined 0.189 r_nbtor_refined 0.186 r_chiral_restr 0.122 r_nbtor_other 0.085 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 232 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction DENZO data reduction SCALEPACK data scaling REFMAC phasing