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1.25 Angstrom Crystal Structure of Chitinase from Bacillus anthracis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N11
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 292 Protein: 16.7 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3);
Screen: PACT (B12), 0.01M Zinc chloride, 0.1M MES (pH 6.0), 20% (w/v) PEG6000.
Cryo: 4M Sodium formate
Crystal Properties Matthews coefficient Solvent content 2.09 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.243 α = 90 b = 94.147 β = 90 c = 243.571 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 MARMOSAIC 300 mm CCD C(111) 2016-06-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.25 30 99.9 0.063 0.063 28.2 7.2 174224 -3 12.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 100 0.552 0.852 3.2 5.5
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3N11 1.252 28.1 165370 8767 99.87 0.11852 0.11743 0.13952 0.1651 RANDOM 15.559
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] 0.07 0.18 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.757 r_sphericity_free 19.126 r_dihedral_angle_4_deg 11.577 r_dihedral_angle_3_deg 10.144 r_sphericity_bonded 7.078 r_dihedral_angle_1_deg 4.367 r_long_range_B_refined 2.575 r_long_range_B_other 1.887 r_rigid_bond_restr 1.422 r_angle_refined_deg 1.337
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.757 r_sphericity_free 19.126 r_dihedral_angle_4_deg 11.577 r_dihedral_angle_3_deg 10.144 r_sphericity_bonded 7.078 r_dihedral_angle_1_deg 4.367 r_long_range_B_refined 2.575 r_long_range_B_other 1.887 r_rigid_bond_restr 1.422 r_angle_refined_deg 1.337 r_scangle_other 1.318 r_scbond_it 1.065 r_scbond_other 1.064 r_mcangle_it 1.034 r_mcangle_other 1.034 r_angle_other_deg 0.867 r_mcbond_it 0.745 r_mcbond_other 0.745 r_chiral_restr 0.082 r_gen_planes_refined 0.022 r_gen_planes_other 0.018 r_bond_refined_d 0.007 r_bond_other_d 0.002 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5062 Nucleic Acid Atoms Solvent Atoms 1091 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing