6I21
Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
---|---|---|---|
Type | Source | Accession Code | Details |
experimental model | PDB | 5A8B |
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 293 | 10-25% PEG 2K or 3K, 100 mM Na Acetate or Na Citrate, pH 4.5 - 4.9 Protein conc 10 mg/ml |
Crystal Data
Unit Cell | |
---|---|
Length ( Å ) | Angle ( ˚ ) |
a = 106.389 | α = 90 |
b = 106.389 | β = 90 |
c = 67.486 | γ = 120 |
Symmetry | |
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Space Group | P 64 2 2 |
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 S 6M | 2017-05-12 | 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) | 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 | 1.5 | 67.48 | 100 | 0.071 | 0.074 | 1 | 18.2 | 20.7 | 36515 | 22.2 |
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 | 1.5 | 1.54 | 100 | 2.595 | 2.725 | 0.644 | 1.3 | 21.3 |
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 | 5A8B | 1.5 | 67.48 | 34209 | 1886 | 98.91 | 0.17476 | 0.17304 | 0.20501 | RANDOM | 26.378 |
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] | |
-0.39 | -0.19 | -0.39 | 1.25 |
RMS Deviations | |
---|---|
Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.594 |
r_sphericity_free | 27.908 |
r_dihedral_angle_3_deg | 14.797 |
r_dihedral_angle_4_deg | 14.495 |
r_sphericity_bonded | 8.616 |
r_dihedral_angle_1_deg | 6.054 |
r_long_range_B_refined | 3.884 |
r_long_range_B_other | 3.883 |
r_rigid_bond_restr | 2.754 |
r_scangle_other | 2.7 |
Non-Hydrogen Atoms Used in Refinement | |
---|---|
Non-Hydrogen Atoms | Number |
Protein Atoms | 1057 |
Nucleic Acid Atoms | |
Solvent Atoms | 129 |
Heterogen Atoms | 110 |
Software
Software | |
---|---|
Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |