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Xylanase T6 (XT6) from Geobacillus Stearothermophilus in complex with xylohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1R86
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 293 30% PEG 4K, 0.01M ZnCl2, 0.1M MES buffer, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.33 63.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.8 α = 90 b = 61.67 β = 119.38 c = 89.35 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 100 IMAGE PLATE RIGAKU RAXIS HTC 2013-09-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 43.07 89.4 4.6 45528 45528
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 49
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) 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 THROUGHOUT 1R86 1.8 43.07 45528 45528 2449 89.42 0.15341 0.15341 0.15126 0.1599 0.19413 0.2 RANDOM 25.617
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] 0.88 -0.2 0.4 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_3_deg 14.615 r_long_range_B_refined 10.432 r_long_range_B_other 9.862 r_dihedral_angle_1_deg 6.779 r_scangle_other 5.476 r_scbond_it 3.663 r_scbond_other 3.633 r_mcangle_other 3.113
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.803 r_dihedral_angle_4_deg 16.001 r_dihedral_angle_3_deg 14.615 r_long_range_B_refined 10.432 r_long_range_B_other 9.862 r_dihedral_angle_1_deg 6.779 r_scangle_other 5.476 r_scbond_it 3.663 r_scbond_other 3.633 r_mcangle_other 3.113 r_mcangle_it 3.107 r_mcbond_it 2.235 r_mcbond_other 2.224 r_angle_refined_deg 2.158 r_angle_other_deg 1.011 r_chiral_restr 0.153 r_bond_refined_d 0.021 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 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 3036 Nucleic Acid Atoms Solvent Atoms 477 Heterogen Atoms 68
Software Software Software Name Purpose HKL-3000 data collection REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling REFMAC phasing