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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with chelerythrine
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 2.29 46.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.37 α = 90 b = 83.61 β = 90 c = 103.77 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 2009-04-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.87933 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 2 19.956 99.8 0.135 12.88 40228 -3 24.202
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 2 2.05 99.9 0.516 0.556 5
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 2 19.956 40227 2012 99.77 0.1556 0.153 0.1528 0.2053 0.2055 RANDOM 19.6941
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] -0.1 0.04 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.583 r_dihedral_angle_3_deg 14.471 r_dihedral_angle_4_deg 12.32 r_dihedral_angle_1_deg 6.461 r_angle_refined_deg 1.862 r_chiral_restr 0.171 r_bond_refined_d 0.025 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4359 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 58
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction