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Crystal Structure Analysis of Hen Egg White Lysozyme Crosslinked by Polymerized Glutaraldehyde in Acidic Environment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other In-House Coordinates
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.8 291 0.1M Sodium Acetate, 7% NaCl, 25% Ethylene glycol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2 38.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.856 α = 90 b = 78.856 β = 90 c = 36.954 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 MAR CCD 165 mm mirrors 2005-09-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
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 1.56 55.73 97.7 0.036 0.036 47.2 7.5 17157 17157 -3
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) 1.56 1.59 87.1 0.367 0.367 2.34 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT In-House Coordinates 1.56 55.73 17157 15912 842 97.66 0.12937 0.1266 0.1313 0.1824 0.1846 RANDOM 30.913
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] -0.19 -0.19 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.618 r_sphericity_free 22.949 r_dihedral_angle_4_deg 17.14 r_scangle_it 16.243 r_scbond_it 14.344 r_sphericity_bonded 14.033 r_dihedral_angle_3_deg 13.32 r_rigid_bond_restr 9.29 r_mcangle_it 8.31 r_mcbond_it 6.628
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.618 r_sphericity_free 22.949 r_dihedral_angle_4_deg 17.14 r_scangle_it 16.243 r_scbond_it 14.344 r_sphericity_bonded 14.033 r_dihedral_angle_3_deg 13.32 r_rigid_bond_restr 9.29 r_mcangle_it 8.31 r_mcbond_it 6.628 r_dihedral_angle_1_deg 5.756 r_angle_refined_deg 1.445 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.289 r_nbd_refined 0.226 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.162 r_chiral_restr 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1097 Nucleic Acid Atoms Solvent Atoms 123 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing