4AC5
Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 7.9 | BATCH CRYSTALLIZATIONS WERE SET UP IN SEPTUM-SEALED GLASS VIALS CONTAINING 100 UL PROTEIN (20-30 MG/ML) , 100 UL LIPIDIC SPONGE PHASE (12 % MONOOLEIN, 17.5 % JEFFAMINE M- 600, 1.0 M HEPES PH 8.0, 0.7 M (NH4)2SO4, 2.5 % 1,2,3- HEPTANETRIOL) AND 50 UL 1.0-1.2 M TRI-SODIUM CITRATE | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.4 | 64 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 57.5 | α = 90 |
| b = 84.6 | β = 90 |
| c = 375.8 | 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 | 288 | CCD | ADSC QUANTUM 315r | 2010-06-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | FREE ELECTRON LASER | SLAC LCLS BEAMLINE AMO | 6.2 | SLAC LCLS | AMO |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 7.4 | 46.1 | 85 | 0.5 | 1.9 | 8 | 2431 | 2 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
| 1 | 7.37 | 7.62 | 21.1 | 1.1 | |||||||||||||||
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 | PDB ENTRY 2WJN | 8.2 | 46.1 | 1899 | 95 | 96.94 | 0.35239 | 0.35071 | 0.384 | RANDOM | 15.401 | ||||||
| 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] | |
| -0.01 | 0.07 | -0.06 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 29.859 |
| r_dihedral_angle_3_deg | 13.54 |
| r_dihedral_angle_4_deg | 9.74 |
| r_dihedral_angle_1_deg | 3.77 |
| r_angle_refined_deg | 1.65 |
| r_scangle_it | 0.089 |
| r_mcangle_it | 0.088 |
| r_chiral_restr | 0.054 |
| r_mcbond_it | 0.049 |
| r_scbond_it | 0.048 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 9185 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | 650 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| CrystFEL | data reduction |
| MONTE | data scaling |
| PHASER | phasing |
