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Structure of the N-terminal CBM22-1-CBM22-2 tandem domain from Paenibacillus barcinonensis Xyn10C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DYO 1DYO and 2w5f experimental model PDB 2W5F 1DYO and 2w5f
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 23% PEG 3350, 0.2 M Calcium chloride, 0.1 M Bis Tris propane pH 5.5
Additive: 2% 1,6-Hexanediol
Ratio (protein/precipitant/additive): 0.5/2/0.3 with streak seeding starting from spherulites.
Crystal Properties Matthews coefficient Solvent content 2.54 51.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.17 α = 90 b = 110.359 β = 90.63 c = 118.522 γ = 90
Symmetry Space Group P 1 21 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 PIXEL DECTRIS PILATUS 6M-F 2013-02-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.979235 ESRF ID29
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 2.43 118.52 99.4 0.13 0.085 8.6 6.3 81116 1 1 37.24
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 2.43 2.48 99.3 0.8 2.2 6.5 5568
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 1DYO and 2w5f 2.43 118.52 77022 4072 99.28 0.22879 0.22687 0.2308 0.26495 0.2657 RANDOM 48.706
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] 0.12 -1.17 -2.43 2.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.587 r_dihedral_angle_4_deg 18.023 r_dihedral_angle_3_deg 14.507 r_long_range_B_refined 8.415 r_long_range_B_other 8.415 r_scangle_other 6.359 r_dihedral_angle_1_deg 5.985 r_mcangle_it 5.407 r_mcangle_other 5.407 r_scbond_it 4.104
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.587 r_dihedral_angle_4_deg 18.023 r_dihedral_angle_3_deg 14.507 r_long_range_B_refined 8.415 r_long_range_B_other 8.415 r_scangle_other 6.359 r_dihedral_angle_1_deg 5.985 r_mcangle_it 5.407 r_mcangle_other 5.407 r_scbond_it 4.104 r_scbond_other 4.103 r_mcbond_it 3.564 r_mcbond_other 3.563 r_angle_other_deg 1.967 r_angle_refined_deg 1.535 r_chiral_restr 0.079 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 12488 Nucleic Acid Atoms Solvent Atoms 30 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing