☰ Navigation Tabs
Flavobacterium johnsoniae GH31 dextranase, FjDex31A, mutant D412A complexed with isomaltotriose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6JR6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM sodium acetate buffer, 8% (w/v) polyethylene glycol 20000, and 8% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 2.91 57.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.37 α = 111.06 b = 112.625 β = 92.98 c = 114.172 γ = 114.54
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 ADSC QUANTUM 315r 2017-12-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1 Photon Factory BL-5A
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 1.8 47.4 96.9 0.054 15.3 2 378141
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 1.8 1.83 95.4 0.4 2 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 6JR6 1.8 47.38 358984 19153 97 0.1512 0.1499 0.161 0.1736 0.1821 RANDOM 20.26
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 15.346 r_dihedral_angle_3_deg 12.016 r_dihedral_angle_1_deg 6.678 r_angle_other_deg 2.374 r_angle_refined_deg 1.78 r_chiral_restr 0.124 r_bond_other_d 0.035 r_bond_refined_d 0.014 r_gen_planes_other 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 15.346 r_dihedral_angle_3_deg 12.016 r_dihedral_angle_1_deg 6.678 r_angle_other_deg 2.374 r_angle_refined_deg 1.78 r_chiral_restr 0.124 r_bond_other_d 0.035 r_bond_refined_d 0.014 r_gen_planes_other 0.009 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26328 Nucleic Acid Atoms Solvent Atoms 3621 Heterogen Atoms 256
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing