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Crystal structure of AbnA (open conformation), a GH43 extracellular arabinanase from Geobacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HO0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 17%-19% PEG 6K, 0.2M NaCl, 0.1M HEPES buffer, pH 7
Crystal Properties Matthews coefficient Solvent content 2.09 41.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.693 α = 90 b = 87.541 β = 90 c = 129.234 γ = 90
Symmetry Space Group P 21 21 21
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 2014-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.976 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 2.36 50 99.1 0.078 10.4 4.3 32247
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.36 2.4 96.5 0.35 3.4 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 5HO0 2.37 47.43 30639 1576 98.52 0.16853 0.16491 0.1698 0.24159 0.24 RANDOM 27.911
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] 3.88 -2.27 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.163 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 16.007 r_dihedral_angle_1_deg 7.169 r_long_range_B_refined 5.19 r_long_range_B_other 5.19 r_scangle_other 3.477 r_mcangle_other 2.949 r_mcangle_it 2.948 r_scbond_it 2.142
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.163 r_dihedral_angle_4_deg 16.742 r_dihedral_angle_3_deg 16.007 r_dihedral_angle_1_deg 7.169 r_long_range_B_refined 5.19 r_long_range_B_other 5.19 r_scangle_other 3.477 r_mcangle_other 2.949 r_mcangle_it 2.948 r_scbond_it 2.142 r_scbond_other 2.141 r_mcbond_it 1.859 r_mcbond_other 1.856 r_angle_refined_deg 1.603 r_angle_other_deg 0.8 r_chiral_restr 0.092 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 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 6312 Nucleic Acid Atoms Solvent Atoms 378 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing