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Crystal structure of thermophilic dextranase from Thermoanaerobacter pseudethanolicus, D312G mutant in complex with isomaltohexaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AXG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.8 293 0.12 M sodium dihydrogenphosphate dihydrate,
1.68 M potassium phosphate dibasic
Crystal Properties Matthews coefficient Solvent content 2.42 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.334 α = 90 b = 99.179 β = 90 c = 169.254 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 95 CCD ADSC QUANTUM 315 2014-06-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 38.92 99.5 0.127 0.122 22.2 13.7 67398 -3
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 2.2 2.28 98.1 0.798 3.6 13.2
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 5AXG 2.2 38.92 63212 3350 98.34 0.16245 0.1602 0.1677 0.20516 0.2102 RANDOM 34.667
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] -0.31 0.01 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.406 r_dihedral_angle_4_deg 16.294 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_1_deg 6.537 r_long_range_B_refined 5.725 r_long_range_B_other 5.684 r_scangle_other 3.905 r_mcangle_it 2.925 r_mcangle_other 2.925 r_scbond_it 2.388
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.406 r_dihedral_angle_4_deg 16.294 r_dihedral_angle_3_deg 13.331 r_dihedral_angle_1_deg 6.537 r_long_range_B_refined 5.725 r_long_range_B_other 5.684 r_scangle_other 3.905 r_mcangle_it 2.925 r_mcangle_other 2.925 r_scbond_it 2.388 r_scbond_other 2.386 r_mcbond_it 1.852 r_mcbond_other 1.851 r_angle_refined_deg 1.367 r_angle_other_deg 0.888 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 9566 Nucleic Acid Atoms Solvent Atoms 594 Heterogen Atoms 144
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing