7QJP
Crystal structure of a cutinase enzyme from Saccharopolyspora flava (611)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 1JFR |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 293 | 20 % PEG 3350, 0.2 M sodium fluoride, 0.1 M Bis-Tris propane pH 6.5 |
Crystal Properties | |
---|---|
Matthews coefficient | Solvent content |
2.94 | 58.17 |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 89.336 | α = 90 |
b = 89.336 | β = 90 |
c = 74.324 | γ = 120 |
Symmetry | |
---|---|
Space Group | P 3 2 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 EIGER2 XE 16M | 2021-05-06 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.8153 | Diamond | I03 |
Data Collection
Overall | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.561 | 77.367 | 94.9 | 0.14 | 0.034 | 0.999 | 12.5 | 17.4 | 40562 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.561 | 1.652 | 2.153 | 0.548 | 0.632 | 1.4 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 1jfr | 1.561 | 77.367 | 40562 | 1981 | 82.749 | 0.142 | 0.1406 | 0.1653 | 21.693 |
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] | |
0.013 | 0.007 | 0.013 | -0.043 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.092 |
r_dihedral_angle_3_deg | 11.036 |
r_dihedral_angle_4_deg | 8.956 |
r_dihedral_angle_1_deg | 6.804 |
r_lrange_it | 5.877 |
r_lrange_other | 5.576 |
r_scangle_it | 2.738 |
r_scangle_other | 2.737 |
r_angle_refined_deg | 2.013 |
r_scbond_it | 1.886 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1949 |
Nucleic Acid Atoms | |
Solvent Atoms | 314 |
Heterogen Atoms | 13 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
autoPROC | data reduction |
STARANISO | data scaling |
MOLREP | phasing |