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The high-resolution crystal structure of ixt6, a thermophilic, intracellular xylanase from G. stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R85 1R85 Initial model of Xylanase T-6 (family10) of G.bacillus stearothermophilus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 1.9M sodium acetate, 0.1M cacodylate pH=6.5, 293.0 K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.48 64.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 169.481 α = 90 b = 80.579 β = 91.89 c = 79.054 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 2001-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C 1.1 NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.45 38 91.6 0.058 18.1 7 187710 171850 18.1 22.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.45 1.48 52.3 0.444 0.342 1.5 5.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 FREE R 1R85 Initial model of Xylanase T-6 (family10) of G.bacillus stearothermophilus 1.45 15 156685 6741 83.5 0.15 0.1499 0.1446 0.1901 0.1787 RANDOM 30.434
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 29 6135.99
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.101 s_non_zero_chiral_vol 0.073 s_zero_chiral_vol 0.059 s_similar_adp_cmpnt 0.037 s_angle_d 0.03 s_from_restr_planes 0.029 s_anti_bump_dis_restr 0.02 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5385 Nucleic Acid Atoms Solvent Atoms 679 Heterogen Atoms 80
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling CNS refinement SHELX refinement PDB_EXTRACT data extraction CNS phasing DENZO data reduction