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Crystal structure of Abp-D197A (a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus), in complex with arabinose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NXK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 293 1.8M Ammonium Sulfate, 0.1M citrate buffer, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.8 67.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.6 α = 90 b = 201.505 β = 90 c = 286.911 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 2013-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.954 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.19 34.71 89 301393 268240
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 2.19 2.25 76.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 4NXK 2.19 34.71 301393 268240 14318 89.04 0.17098 0.16847 0.1758 0.21888 0.2216 RANDOM 34.962
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] -1.48 2.96 -1.48
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.584 r_dihedral_angle_4_deg 18.757 r_dihedral_angle_3_deg 16.634 r_long_range_B_refined 8.59 r_long_range_B_other 8.576 r_dihedral_angle_1_deg 7.527 r_scangle_other 5.8 r_mcangle_it 4.895 r_mcangle_other 4.895 r_scbond_it 3.947
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.584 r_dihedral_angle_4_deg 18.757 r_dihedral_angle_3_deg 16.634 r_long_range_B_refined 8.59 r_long_range_B_other 8.576 r_dihedral_angle_1_deg 7.527 r_scangle_other 5.8 r_mcangle_it 4.895 r_mcangle_other 4.895 r_scbond_it 3.947 r_scbond_other 3.922 r_mcbond_it 3.347 r_mcbond_other 3.346 r_angle_refined_deg 1.988 r_angle_other_deg 0.948 r_chiral_restr 0.126 r_bond_refined_d 0.019 r_gen_planes_refined 0.01 r_bond_other_d 0.001 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 27794 Nucleic Acid Atoms Solvent Atoms 2932 Heterogen Atoms 688
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling