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Crystal structure of native xylanase 10B from Thermotoga petrophila RKU-1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.3 291 PEG8000
glycerol
sodium acetate
litium sulfate, pH 4.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.538 α = 84.54 b = 58.554 β = 70.82 c = 61.579 γ = 68.87
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 2010-05-03 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 1.58 31.24 92.8 0.101 95840 91930 3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.58 1.64 86.8
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.58 31.24 87311 4584 92.5 0.1598 0.15792 0.1563 0.19551 0.1938 RANDOM 16.641
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] -0.37 -0.01 -0.09 0.18 -0.47 0.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.943 r_dihedral_angle_4_deg 20.297 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 6.279 r_scangle_it 6.16 r_scbond_it 3.865 r_mcangle_it 2.463 r_angle_refined_deg 2.415 r_mcbond_it 1.518 r_chiral_restr 0.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.943 r_dihedral_angle_4_deg 20.297 r_dihedral_angle_3_deg 13.328 r_dihedral_angle_1_deg 6.279 r_scangle_it 6.16 r_scbond_it 3.865 r_mcangle_it 2.463 r_angle_refined_deg 2.415 r_mcbond_it 1.518 r_chiral_restr 0.187 r_bond_refined_d 0.03 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5440 Nucleic Acid Atoms Solvent Atoms 616 Heterogen Atoms 45
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling