8B3Y
Native Thermogutta terrifontis endoglucanase catalytic domain with a linker at C-terminal from glycoside hydrolase family 5 (TtEnd5A-CDC)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 8AG9 |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 6.5 | 293.15 | Well number B2 conditions of LMB screen: 1.9M Ammonium Sulphate, 0.1M MES pH 6.5 + Additive Screen (well number C11 conditions of Grid Screen Salt HR2-248: 2.9 M Sodium malonate pH 5.0) TtEnd5A CD-C variant = 10.6 mg/ml. 10x Cellobiose (100 uM) |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.2 | 44.16 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 59.98 | α = 90 |
b = 69.52 | β = 90 |
c = 81.28 | 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 | 100 | PIXEL | DECTRIS EIGER2 XE 16M | 2021-04-22 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | 0.9795 | Diamond | I04 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 1.25 | 48.26 | 99 | 0.055 | 0.059 | 0.017 | 1 | 15.7 | 12 | 93566 | 16.21 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 1.25 | 1.28 | 90.4 | 2.076 | 2.183 | 0.952 | 0.348 | 5.4 |
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 | 8AG9 | 1.25 | 48.26 | 88862 | 4586 | 98.88 | 0.13793 | 0.13679 | 0.16052 | RANDOM | 20.33 |
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] | |
0.89 | -1.2 | 0.31 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 30.325 |
r_dihedral_angle_4_deg | 20.237 |
r_dihedral_angle_3_deg | 11.526 |
r_dihedral_angle_1_deg | 6.083 |
r_long_range_B_refined | 3.071 |
r_scangle_other | 2.973 |
r_long_range_B_other | 2.923 |
r_scbond_it | 2.399 |
r_scbond_other | 2.387 |
r_rigid_bond_restr | 2.319 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 2732 |
Nucleic Acid Atoms | |
Solvent Atoms | 236 |
Heterogen Atoms | 15 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
Coot | model building |
MOLREP | phasing |
PDB-REDO | refinement |
xia2 | data reduction |
xia2 | data scaling |