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Crystal structure of Ara127N-Se, a GH127 beta-L-arabinofuranosidase from Geobacillus Stearothermophilus T6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 20% PEG3350, 1% Tryptone, 0.1 M HEPES sodium, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.32 47.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.383 α = 90 b = 132.266 β = 113.06 c = 109.045 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 100 CCD MARMOSAIC 225 mm CCD 2014-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.978 ESRF BM14
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 2.258 40 99.53 0.123 6.7 7.1 122372 121797 -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 2.258 2.29 94.23 3.2 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.258 40 122372 121797 6452 99.53 0.15965 0.15965 0.15748 0.1697 0.20048 0.2065 RANDOM 34.756
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] -2.02 -1.47 1.2 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.248 r_dihedral_angle_4_deg 16.562 r_dihedral_angle_3_deg 16.21 r_long_range_B_refined 8.748 r_long_range_B_other 8.7 r_scangle_other 6.518 r_dihedral_angle_1_deg 6.157 r_mcangle_it 4.813 r_mcangle_other 4.813 r_scbond_it 4.195
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.248 r_dihedral_angle_4_deg 16.562 r_dihedral_angle_3_deg 16.21 r_long_range_B_refined 8.748 r_long_range_B_other 8.7 r_scangle_other 6.518 r_dihedral_angle_1_deg 6.157 r_mcangle_it 4.813 r_mcangle_other 4.813 r_scbond_it 4.195 r_scbond_other 4.195 r_mcbond_it 3.222 r_mcbond_other 3.218 r_angle_refined_deg 1.645 r_angle_other_deg 1.28 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.011 r_bond_other_d 0.008 r_gen_planes_other 0.007 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 20588 Nucleic Acid Atoms Solvent Atoms 1518 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data collection AutoSol phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling