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Crystal Structure Analysis of Chitinase A from Vibrio harveyi with novel inhibitors - W275G mutant complex structure with DEQUALINIUM
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 2.26 45.48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.6 α = 90 b = 84.15 β = 90 c = 102.6 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 IMAGE PLATE MARRESEARCH helios mirrors 2009-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.23 19.936 98.3 0.082 17.64 28235 -3 23.618
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 2.23 2.29 84.3 0.39 0.447 4.6
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 2.23 19.936 28235 1412 100 0.1649 0.1616 0.1608 0.2287 0.2242 RANDOM 16.7136
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] -0.01 -0.28 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.079 r_dihedral_angle_4_deg 18.693 r_dihedral_angle_3_deg 15.658 r_dihedral_angle_1_deg 6.666 r_scangle_it 4.333 r_scbond_it 2.917 r_angle_refined_deg 1.765 r_mcangle_it 1.671 r_mcbond_it 0.952 r_chiral_restr 0.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.079 r_dihedral_angle_4_deg 18.693 r_dihedral_angle_3_deg 15.658 r_dihedral_angle_1_deg 6.666 r_scangle_it 4.333 r_scbond_it 2.917 r_angle_refined_deg 1.765 r_mcangle_it 1.671 r_mcbond_it 0.952 r_chiral_restr 0.128 r_bond_refined_d 0.021 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4359 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 108
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction