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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant 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 5.5 293 26%(w/v) PEG 4000, 0.2M Ammonium Acetate, 0.1M Sodium Acetate, pH 5.5, hanging drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.25 45.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.67 α = 90 b = 83.93 β = 90 c = 102.42 γ = 90
Symmetry Space Group P 21 21 21
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 2009-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.999989 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 1.9 19.901 99.8 0.12 18.02 45919 -3 20.141
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 1.9 1.95 100 0.362 0.389 7.8
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 1.9 19.9 45918 2296 99.82 0.1461 0.1435 0.1435 0.195 0.1945 RANDOM 16.1011
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] -0.16 -0.1 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.193 r_dihedral_angle_3_deg 13.656 r_dihedral_angle_4_deg 11.881 r_dihedral_angle_1_deg 6.345 r_angle_refined_deg 2.013 r_chiral_restr 0.179 r_bond_refined_d 0.024 r_gen_planes_refined 0.011
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4359 Nucleic Acid Atoms Solvent Atoms 631 Heterogen Atoms 60
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction