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High resolution structure of the thermostable glucuronoxylan endo-Beta-1, 4-xylanase, CtXyn30A, from Clostridium thermocellum with two xylobiose units bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4UQE PDBE ENTRY 4UQE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.2 M POTASSIUM PHOSPHATE
Crystal Properties Matthews coefficient Solvent content 2.57 52.25
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.133 α = 90 b = 87.249 β = 114.68 c = 60.027 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 2014-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 SOLEIL PROXIMA 1
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 1.8 46.25 100 0.28 17.5 3.8 43517 9.8
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 1.8 1.84 100 1.49 9.8 3.8
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 PDBE ENTRY 4UQE 1.8 54.54 41363 2128 99.97 0.13712 0.1358 0.1489 0.16242 0.1734 RANDOM 9.888
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] 0.01 -0.16 0.18 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.338 r_dihedral_angle_4_deg 20.189 r_dihedral_angle_3_deg 11.678 r_dihedral_angle_1_deg 6.613 r_angle_refined_deg 1.763 r_angle_other_deg 1.023 r_scbond_it 0.91 r_mcangle_it 0.731 r_mcbond_it 0.419 r_mcbond_other 0.417
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.338 r_dihedral_angle_4_deg 20.189 r_dihedral_angle_3_deg 11.678 r_dihedral_angle_1_deg 6.613 r_angle_refined_deg 1.763 r_angle_other_deg 1.023 r_scbond_it 0.91 r_mcangle_it 0.731 r_mcbond_it 0.419 r_mcbond_other 0.417 r_chiral_restr 0.109 r_bond_refined_d 0.018 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3114 Nucleic Acid Atoms Solvent Atoms 404 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing