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Crystal structure of Abp-D197A, a catalytic mutant of a GH27-b-L-arabinopyranosidase from Geobacillus stearothermophilus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NX0
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 3.84 67.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.701 α = 90 b = 203.525 β = 90 c = 286.946 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 2012-09-11 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 2.3 24.86 97.1 269263 255755
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 2.3 2.34 96.32 0.086 8.3 5.5
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 4NX0 2.3 24.86 269263 255755 13611 96.32 0.17109 0.17109 0.16953 0.1756 0.20069 0.2039 RANDOM 36.362
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] -3.09 4.21 -1.12
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.285 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 15.587 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 1.841 r_angle_other_deg 1.722 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.013
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.285 r_dihedral_angle_4_deg 17.201 r_dihedral_angle_3_deg 15.587 r_dihedral_angle_1_deg 6.94 r_angle_refined_deg 1.841 r_angle_other_deg 1.722 r_chiral_restr 0.13 r_bond_refined_d 0.019 r_gen_planes_refined 0.014 r_bond_other_d 0.013 r_gen_planes_other 0.011 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27776 Nucleic Acid Atoms Solvent Atoms 3062 Heterogen Atoms 588
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling