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The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Native structure to 1.9
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 154L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 48-53% ammonium sulphate, 5mM CoCl2, 0.1M BisTris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.95 36.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.12 α = 90 b = 75.39 β = 92.92 c = 78.37 γ = 90
Symmetry Space Group C 1 2 1
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 MARMOSAIC 225 mm CCD 2007-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1
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 1.9 48.02 99.5 0.06 0.06 9.4 4.5 50454 50202 2 18.99
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) 1.9 2 96.9 0.221 0.221 3.3 4.3 7068
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 154L 1.9 48.02 47647 2548 99.53 0.19412 0.19108 0.191 0.25136 0.2506 RANDOM 18.764
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] 0.53 -1.58 -0.79 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.841 r_dihedral_angle_4_deg 20.667 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_1_deg 6.108 r_scangle_it 3.895 r_scbond_it 2.658 r_mcangle_it 1.646 r_angle_refined_deg 1.563 r_mcbond_it 1.083 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.841 r_dihedral_angle_4_deg 20.667 r_dihedral_angle_3_deg 16.314 r_dihedral_angle_1_deg 6.108 r_scangle_it 3.895 r_scbond_it 2.658 r_mcangle_it 1.646 r_angle_refined_deg 1.563 r_mcbond_it 1.083 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.214 r_symmetry_hbond_refined 0.187 r_xyhbond_nbd_refined 0.166 r_chiral_restr 0.118 r_bond_refined_d 0.019 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5731 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 2
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling