6ZID
Ultrafast Structural Response to Charge Redistribution Within a Photosynthetic Reaction Centre - 5 ps (b) structure
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2I5N |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 277 | Macrocrystal growth: 10 mg/ml protein, 3.6 M ammonium sulphate, 6 % w/v heptane-1,2,3-triol, 20 mM KH203/K2H03 pH 6.8, 0.1 % LDAO 20 ul sitting drop, 10 protein : 10 precipitant Microcrystals: 8.5 mg/ml protein 18.5 ul sitting drop, 10 protein : 7.5 precipitant : 1 seed stock |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 226.5 | α = 90 |
b = 226.5 | β = 90 |
c = 113.9 | γ = 90 |
Symmetry | |
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Space Group | P 43 21 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 293 | PIXEL | CS-PAD CXI-1 | 2016-06-13 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE CXI | 1.3 | SLAC LCLS | CXI |
Serial Crystallography
Sample delivery method | ||
---|---|---|
Diffraction ID | Description | Sample Delivery Method |
1 | injection |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | 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 | 2.8 | 35.8 | 100 | 0.998 | 16.42 | 5350 | 75091 | 98.13 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.8 | 2.83 | 0.908 | 2.33 |
Refinement
Statistics | |||||||||||||||||||
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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 | 2I5N | 2.8 | 34.31 | 1.34 | 73081 | 3635 | 99.95 | 0.1606 | 0.1594 | 0.1832 | 92.72 |
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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 21.0782 |
f_angle_d | 2.089 |
f_chiral_restr | 0.0634 |
f_plane_restr | 0.0102 |
f_bond_d | 0.0083 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9347 |
Nucleic Acid Atoms | |
Solvent Atoms | 146 |
Heterogen Atoms | 909 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
PHENIX | refinement |
CrystFEL | data reduction |
CrystFEL | data scaling |
PHASER | phasing |