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Crystal structure of endo-arabinanase ABN-TS D27A mutant in complex with arabinotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WL7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 20% PEG 8000, 0.2M magnesium chloride, 0.1M Tris-HCl pH 8.5
Crystal Properties Matthews coefficient Solvent content 1.88 34.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.125 α = 90 b = 77.032 β = 90 c = 88.701 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 RIGAKU JUPITER 210 2008-07-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) 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 1.65 50 99.9 0.019 34.4 9.8 33864
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.65 1.68 99.6 0.178 3.95 8.2
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 1WL7 1.65 44.35 32149 1658 99.91 0.14944 0.14715 0.1593 0.195 0.2 RANDOM 25.541
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_4_deg 20.726 r_dihedral_angle_3_deg 13.033 r_long_range_B_refined 7.293 r_dihedral_angle_1_deg 7.199 r_long_range_B_other 7.187 r_scangle_other 5.464 r_scbond_it 3.87 r_scbond_other 3.844 r_mcangle_other 3.333
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.208 r_dihedral_angle_4_deg 20.726 r_dihedral_angle_3_deg 13.033 r_long_range_B_refined 7.293 r_dihedral_angle_1_deg 7.199 r_long_range_B_other 7.187 r_scangle_other 5.464 r_scbond_it 3.87 r_scbond_other 3.844 r_mcangle_other 3.333 r_mcangle_it 3.332 r_mcbond_it 2.336 r_mcbond_other 2.318 r_angle_refined_deg 2.267 r_angle_other_deg 1.108 r_chiral_restr 0.154 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.007 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 2523 Nucleic Acid Atoms Solvent Atoms 266 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing