6GS0
Native Glucuronoyl Esterase from Opitutus terrae
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 6GRW |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293.15 | Reservoir composition: 0.3 M Sodium phosphate dibasic dihydrate, 0.3 M Ammonium sulfate and 0.3 M Sodium nitrate, 0.05 M Tris and 0,05 M BICINE, 12.5 % v/v MPD, 12.5 % w/v PEG1000 and 12.5 % w/v PEG3350 Drop size and composition: sitting drops of 0.3 ul were mixed in a protein:reservoir volume ratio of 3:1 using 45 mg/ml of OtCE15A in 20 mM TRIS pH 8.0 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
1.9 | 35.26 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 43.361 | α = 75.863 |
b = 44.263 | β = 66.326 |
c = 50.027 | γ = 70.876 |
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 | PIXEL | DECTRIS PILATUS3 6M | 2017-04-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID30B | 0.9 | ESRF | ID30B |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | 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 | 1.34 | 45.43 | 88.9 | 0.092 | 0.101 | 0.995 | 6.35 | 2.95 | 63925 | 14.79 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.34 | 1.37 | 88.6 | 1.073 | 1.159 | 0.534 | 0.97 | 2.93 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | Mean Isotropic B | ||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 6GRW | 1.34 | 45.43 | 1.94 | 63886 | 2645 | 89.06 | 0.1745 | 0.173 | 0.2073 | 22.56 |
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 |
f_dihedral_angle_d | 18.3092 |
f_angle_d | 1.0739 |
f_chiral_restr | 0.0749 |
f_plane_restr | 0.0086 |
f_bond_d | 0.0081 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 3074 |
Nucleic Acid Atoms | |
Solvent Atoms | 366 |
Heterogen Atoms | 52 |
Software
Software | |
---|---|
Software Name | Purpose |
PHENIX | refinement |
Coot | model building |
XDS | data reduction |
PHENIX | phasing |
XDS | data scaling |