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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - complex structure with PENTOXIFYLLINE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3B9A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging drop 8.5 293 1.1M Ammonium Sulfate, 0.1M Tris, pH 8.5, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.33 47.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.02 α = 90 b = 85.34 β = 112.9 c = 62.97 γ = 90
Symmetry Space Group P 1 21 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 2009-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9840 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.65 19.948 97.2 0.07 12.34 68396 -3 23.031
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.69 97.8 0.47 0.564 3.7
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 3b9a 1.65 19.948 68395 3420 97.31 0.1456 0.1434 0.1434 0.1878 0.1878 RANDOM 19.2401
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] -0.41 -0.34 -0.33 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.868 r_dihedral_angle_4_deg 13.93 r_dihedral_angle_3_deg 13.77 r_dihedral_angle_1_deg 6.077 r_angle_refined_deg 2.368 r_chiral_restr 0.189 r_bond_refined_d 0.029 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4354 Nucleic Acid Atoms Solvent Atoms 697 Heterogen Atoms 40
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction