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Crystal Structures of Clostridium thermocellum Xyloglucanase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1SQJ PDB ENTRY 1SQJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5MM CDCL2, 12% PEG 4K, NA CACODYLATE PH 6.5
Crystal Properties Matthews coefficient Solvent content 3.03 59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.437 α = 90 b = 97.941 β = 97.62 c = 199.122 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 120 CCD MARRESEARCH 2004-12-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 ESRF ID14-3
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 2.1 45.79 99 0.12 9.9 3.9 220410 2
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 2.1 2.21 98.3 0.52 2.5 3.9
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 PDB ENTRY 1SQJ 2.1 19.9 208964 11183 98.8 0.178 0.176 0.1762 0.21 0.2091 RANDOM 19.36
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 0.02 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 15.71 r_dihedral_angle_3_deg 13.355 r_dihedral_angle_1_deg 7.194 r_scangle_it 2.182 r_scbond_it 1.437 r_angle_refined_deg 1.327 r_mcangle_it 0.892 r_mcbond_it 0.577 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.612 r_dihedral_angle_4_deg 15.71 r_dihedral_angle_3_deg 13.355 r_dihedral_angle_1_deg 7.194 r_scangle_it 2.182 r_scbond_it 1.437 r_angle_refined_deg 1.327 r_mcangle_it 0.892 r_mcbond_it 0.577 r_nbtor_refined 0.304 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.199 r_symmetry_hbond_refined 0.176 r_xyhbond_nbd_refined 0.124 r_chiral_restr 0.097 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other 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 21779 Nucleic Acid Atoms Solvent Atoms 2081 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing