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Crystal structure of S. marcescens chitinase B in complex with the cyclic dipeptide inhibitor cyclo-(Gly-L-Pro) at 2.1 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1O6I WWPDB 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 2.47 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.07 α = 90 b = 103.906 β = 90 c = 186.439 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 2.1 20 89.7 0.07 22.79 3.22 57855 1 20.5
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 2.1 2.18 90.9 0.26 5.3
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 WWPDB ENTRY 1O6I 2.1 24.91 57797 581 48.1 0.199 0.199 0.1943 0.249 0.2407 RANDOM 29.46
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] 0.86 3.18 -4.04
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.86 c_scbond_it 2.15 c_mcangle_it 2.12 c_mcbond_it 1.49 c_angle_deg 1.45177 c_bond_d 0.009586 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na
RMS Deviations Key Refinement Restraint Deviation c_scangle_it 2.86 c_scbond_it 2.15 c_mcangle_it 2.12 c_mcbond_it 1.49 c_angle_deg 1.45177 c_bond_d 0.009586 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 7815 Nucleic Acid Atoms Solvent Atoms 949 Heterogen Atoms 172
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing