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THE TETRA-MODULAR CELLULOSOMAL ARABINOXYLANASE CtXyl5A STRUCTURE AS REVEALED BY X-RAY CRYSTALLOGRAPHY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Y8K PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S experimental model PDB 3MPC PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S experimental model PDB 2Y8M PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S experimental model PDB 2Y9I PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S experimental model PDB 2Y9S PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 40% (V/V) 2-METHYL-2-4PENTANEDIOL (MPD), pH 7
Crystal Properties Matthews coefficient Solvent content 3.66 68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 147.41 α = 90 b = 191.73 β = 90 c = 50.7 γ = 90
Symmetry Space Group P 21 21 2
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 2009-12-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.64 50.7 98.5 0.16 8 5.8 42246
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 2.64 2.78 96.4 0.7 2 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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRIES 2Y8K, 3MPC, 2Y8M, 2Y9I AND 2Y9S 2.64 50.7 40074 2125 97.7 0.23928 0.23726 0.2395 0.278 0.2804 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 15.971 r_dihedral_angle_3_deg 12.726 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 3.755 r_long_range_B_other 3.575 r_mcangle_it 1.411 r_mcangle_other 1.411 r_angle_refined_deg 1.211 r_scangle_other 1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.391 r_dihedral_angle_4_deg 15.971 r_dihedral_angle_3_deg 12.726 r_dihedral_angle_1_deg 6.356 r_long_range_B_refined 3.755 r_long_range_B_other 3.575 r_mcangle_it 1.411 r_mcangle_other 1.411 r_angle_refined_deg 1.211 r_scangle_other 1.12 r_angle_other_deg 0.886 r_mcbond_it 0.765 r_mcbond_other 0.765 r_scbond_it 0.646 r_scbond_other 0.646 r_chiral_restr 0.071 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5446 Nucleic Acid Atoms Solvent Atoms 227 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing