☰ Navigation Tabs
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. Structure with NAG to 1.7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3GXK
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 36.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 110.19 α = 90 b = 75.52 β = 93.25 c = 78.29 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 2008-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
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 1.7 34 99.3 0.062 0.062 7.8 3.7 70454 69961 2 2 22.34
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 1.7 1.79 95.6 0.353 0.353 2.9 3.4
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3GXK 1.7 34 66412 3525 99.25 0.20611 0.20369 0.25231 0.2641 RANDOM 21.496
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 -1.68 -0.84 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.893 r_dihedral_angle_4_deg 18.932 r_dihedral_angle_3_deg 16.427 r_dihedral_angle_1_deg 6.235 r_scangle_it 4.431 r_scbond_it 2.924 r_mcangle_it 1.824 r_angle_refined_deg 1.823 r_mcbond_it 1.107 r_chiral_restr 0.141
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.893 r_dihedral_angle_4_deg 18.932 r_dihedral_angle_3_deg 16.427 r_dihedral_angle_1_deg 6.235 r_scangle_it 4.431 r_scbond_it 2.924 r_mcangle_it 1.824 r_angle_refined_deg 1.823 r_mcbond_it 1.107 r_chiral_restr 0.141 r_bond_refined_d 0.02 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5731 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 187
Software Software Software Name Purpose MAR345 data collection MOLREP phasing REFMAC refinement XDS data reduction SCALA data scaling