6JR8
Flavobacterium johnsoniae GH31 dextranase, FjDex31A, mutant D412A complexed with isomaltotriose
X-RAY DIFFRACTION
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 |
Symmetry | |
---|---|
Space Group | P 1 |
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 | R-Free | 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 | 0.1736 | 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 |
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 |