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Crystal structure of putative chitinase II from Klebsiella pneumoniae
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ITX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.2 289 0.2 M NaCl, 0.1 M Na2HPO4/KH2PO4, 10% PEG8K, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3 58.95
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.341 α = 90 b = 110.672 β = 90 c = 108.481 γ = 90
Symmetry Space Group C 2 2 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 ADSC QUANTUM 315r MIRRORS 2010-10-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID APS 19-ID
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 2.6 50 99.9 0.125 14.7 5.5 17383 -3
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) 2.6 2.64 99.7 0.633 2.1 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 MR-SAD THROUGHOUT 1ITX 2.6 49.29 17288 17287 872 99.41 0.18108 0.17946 0.181 0.21163 0.2112 RANDOM 36.706
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] -1.65 0.84 0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.894 r_dihedral_angle_4_deg 18.799 r_dihedral_angle_3_deg 15.425 r_dihedral_angle_1_deg 5.724 r_scangle_it 2.789 r_scbond_it 1.74 r_angle_refined_deg 1.357 r_mcangle_it 0.967 r_angle_other_deg 0.897 r_mcbond_it 0.489
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.894 r_dihedral_angle_4_deg 18.799 r_dihedral_angle_3_deg 15.425 r_dihedral_angle_1_deg 5.724 r_scangle_it 2.789 r_scbond_it 1.74 r_angle_refined_deg 1.357 r_mcangle_it 0.967 r_angle_other_deg 0.897 r_mcbond_it 0.489 r_mcbond_other 0.094 r_chiral_restr 0.076 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3059 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 18
Software Software Software Name Purpose REFMAC refinement Auto-Rickshaw phasing CNS refinement SBC-Collect data collection PHASER phasing MLPHARE phasing pirate phasing SHELXE model building RESOLVE model building BUCCANEER model building PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling CNS phasing REFMAC phasing RESOLVE phasing BUCCANEER phasing