☰ Navigation Tabs
Crystal structure of AbnA, a GH43 extracellular arabinanase from Geobacillus stearothermophilus, in complex with arabinopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HO2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 17%-19% PEG 6K, 0.2M NaCl, 0.1M HEPES buffer, pH 7
Crystal Properties Matthews coefficient Solvent content 2.13 42.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.459 α = 90 b = 87.786 β = 90 c = 129.908 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 0.98 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 2.95 50 100 0.2 5.1 12.4 17409
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 2.95 3 100 0.7 3.6 10.5
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 5HO2 2.96 47.8 16471 879 99.79 0.17282 0.16801 0.1719 0.25932 0.2601 RANDOM 33.111
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] -0.22 1.17 -0.95
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.529 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 17.986 r_dihedral_angle_1_deg 7.468 r_long_range_B_refined 5.219 r_long_range_B_other 5.204 r_scangle_other 3.085 r_mcangle_other 3.027 r_mcangle_it 3.026 r_scbond_it 1.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.529 r_dihedral_angle_4_deg 18.55 r_dihedral_angle_3_deg 17.986 r_dihedral_angle_1_deg 7.468 r_long_range_B_refined 5.219 r_long_range_B_other 5.204 r_scangle_other 3.085 r_mcangle_other 3.027 r_mcangle_it 3.026 r_scbond_it 1.873 r_scbond_other 1.873 r_mcbond_it 1.862 r_mcbond_other 1.86 r_angle_refined_deg 1.602 r_angle_other_deg 0.82 r_chiral_restr 0.083 r_bond_refined_d 0.013 r_gen_planes_refined 0.006 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 142 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing