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The structure of chi1, a chitinase from Yersinia entomophaga
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ITX PDB ENTRY 1ITX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 7% PEG 1000, 6% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.24 45.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.012 α = 102.85 b = 67.172 β = 108.06 c = 81.679 γ = 92.1
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 2009-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON AUSTRALIAN SYNCHROTRON BEAMLINE MX2 1.03317 Australian Synchrotron MX2
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 1.74 75.27 96.9 0.093 7.7 3.8 110418 110418
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 1.74 1.84 95.7 0.491 2 3.9 15967
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 (All) 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 1ITX 1.74 75.27 104841 104841 5541 96.88 0.16678 0.16678 0.16452 0.1647 0.20989 0.2094 RANDOM 22.089
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] -0.21 -0.4 1.23 -0.71 -0.42 1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_3_deg 12.259 r_dihedral_angle_4_deg 11.403 r_dihedral_angle_1_deg 6.695 r_scangle_it 4.86 r_scbond_it 3.402 r_mcangle_it 2.226 r_angle_refined_deg 1.628 r_mcbond_it 1.473 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.246 r_dihedral_angle_3_deg 12.259 r_dihedral_angle_4_deg 11.403 r_dihedral_angle_1_deg 6.695 r_scangle_it 4.86 r_scbond_it 3.402 r_mcangle_it 2.226 r_angle_refined_deg 1.628 r_mcbond_it 1.473 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7991 Nucleic Acid Atoms Solvent Atoms 835 Heterogen Atoms 60
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement XDS data reduction XDS data scaling