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Crystal Structure of Chitinase ChiW from Paenibacillus sp. str. FPU-7 Reveals a Novel Type of Bacterial Cell-Surface-Expressed Multi-Modular Enzyme Machinery
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 VAPOR DIFFUSION, SITTING DROP 5.5 293 (NH4)2HPO4, Na-citrate
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 111.981 α = 90 b = 127.99 β = 90 c = 162.078 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 CCD ADSC QUANTUM 315 2011-11-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.9 Photon Factory BL-17A
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 2.03 50.01 99 0.058 51.4 7.1 149010
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 2.03 2.07 100 0.363 6.82 6.9
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 1itx 2.03 50.01 141163 7476 98.82 0.18456 0.18235 0.19 0.22581 0.2298 RANDOM 31.072
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] -0.08 0.14 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.865 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 15.97 r_dihedral_angle_1_deg 7.269 r_long_range_B_refined 6.807 r_long_range_B_other 6.751 r_scangle_other 5.051 r_mcangle_it 4.117 r_mcangle_other 4.117 r_scbond_it 3.407
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.865 r_dihedral_angle_4_deg 17.912 r_dihedral_angle_3_deg 15.97 r_dihedral_angle_1_deg 7.269 r_long_range_B_refined 6.807 r_long_range_B_other 6.751 r_scangle_other 5.051 r_mcangle_it 4.117 r_mcangle_other 4.117 r_scbond_it 3.407 r_scbond_other 3.406 r_mcbond_it 2.967 r_mcbond_other 2.966 r_angle_refined_deg 2.011 r_angle_other_deg 1.132 r_chiral_restr 0.132 r_bond_refined_d 0.02 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13463 Nucleic Acid Atoms Solvent Atoms 1322 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing