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Flavobacterium johnsoniae GH31 dextranase, FjDex31A, complexed with glucose
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 57.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.591 α = 87.05 b = 102.602 β = 113.07 c = 114.13 γ = 118.53
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 270 2016-06-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 1.75 35.2 94.8 0.05 20.5 1.8 430825
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 1.75 1.78 88 0.353 2.5 1.7
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 1.75 35.15 384478 20212 95.16 0.1633 0.1622 0.1757 0.1855 0.1968 RANDOM 23.002
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 34.045 r_dihedral_angle_4_deg 14.762 r_dihedral_angle_3_deg 11.963 r_dihedral_angle_1_deg 6.637 r_angle_other_deg 2.34 r_angle_refined_deg 1.736 r_chiral_restr 0.12 r_bond_other_d 0.035 r_bond_refined_d 0.013 r_gen_planes_other 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.045 r_dihedral_angle_4_deg 14.762 r_dihedral_angle_3_deg 11.963 r_dihedral_angle_1_deg 6.637 r_angle_other_deg 2.34 r_angle_refined_deg 1.736 r_chiral_restr 0.12 r_bond_other_d 0.035 r_bond_refined_d 0.013 r_gen_planes_other 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26340 Nucleic Acid Atoms Solvent Atoms 3345 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing