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Crystal structure of xylanase 10B from Thermotoga petrophila RKU-1 in complex with xylobiose
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.3 291 PEG 8000, glycerol, litium sulfate, sodium acetate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.338 α = 84.9 b = 58.576 β = 70.86 c = 61.659 γ = 68.93
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 MARMOSAIC 225 mm CCD 2010-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.458 LNLS W01B-MX2
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 1.9 31.28 94.1 0.112 56289 53633 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.9 1.97 92.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.88 31.28 48525 2581 86.69 0.23395 0.23055 0.29852 0.3013 RANDOM 17.601
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] -0.25 0.1 0.09 0.03 -0.15 0.11
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.111 r_dihedral_angle_4_deg 17.803 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_1_deg 7.199 r_scangle_it 4.482 r_scbond_it 3.028 r_angle_refined_deg 1.864 r_mcangle_it 1.741 r_mcbond_it 1.079 r_chiral_restr 0.137
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.111 r_dihedral_angle_4_deg 17.803 r_dihedral_angle_3_deg 15.94 r_dihedral_angle_1_deg 7.199 r_scangle_it 4.482 r_scbond_it 3.028 r_angle_refined_deg 1.864 r_mcangle_it 1.741 r_mcbond_it 1.079 r_chiral_restr 0.137 r_bond_refined_d 0.023 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5454 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 66
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling