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Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(L-Arg-L-Pro) at 1.85 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6I PDB ENTRY 1O6I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.5 M AMMONIUM SULPHATE, 0.1 M HEPES PH 7, 25 % GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.43 48
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.744 α = 90 b = 103.256 β = 90 c = 185.689 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 RIGAKU RAXIS-IV MIRRORS M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 1.85 25 95.5 0.05 30.1 3.11 88471 18.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.85 1.92 76.1 0.18 6.96
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 PDB ENTRY 1O6I 1.85 24.87 88331 894 95.7 0.187 0.187 0.1804 0.213 0.206 RANDOM 28.47
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] 1.06 9.84 -10.9
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.81 c_scbond_it 2.17 c_mcangle_it 2.02 c_angle_deg 1.58 c_mcbond_it 1.51 c_bond_d 0.012 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.81 c_scbond_it 2.17 c_mcangle_it 2.02 c_angle_deg 1.58 c_mcbond_it 1.51 c_bond_d 0.012 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7803 Nucleic Acid Atoms Solvent Atoms 707 Heterogen Atoms 232
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing