3ZFV
Crystal structure of an archaeal CRISPR-associated Cas6 nuclease
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | 9.1 | 0.05 M BICINE PH 9.1, 28 % PEG3350 | ||
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.88 | 57 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 71.65 | α = 90 |
| b = 127.46 | β = 110.48 |
| c = 83.62 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 1 21 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 | CCD | ADSC QUANTUM 315r | 2012-11-23 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | ESRF BEAMLINE ID14-4 | ESRF | ID14-4 | |
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 | 2.8 | 78.33 | 99.9 | 0.07 | 23.3 | 10.4 | 34686 | 2 | |||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
| 1 | 2.8 | 2.87 | 99.1 | 0.71 | 3.7 | 10.2 | |||||||||||||
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 | SAD | THROUGHOUT | NONE | 2.8 | 78.33 | 32914 | 1750 | 99.78 | 0.20616 | 0.20457 | 0.23557 | RANDOM | 52.402 | ||||||
| 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] | |
| -0.02 | 0.32 | -0.12 | 0.37 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 32.641 |
| r_dihedral_angle_4_deg | 18.894 |
| r_dihedral_angle_3_deg | 15.392 |
| r_dihedral_angle_1_deg | 6.32 |
| r_angle_refined_deg | 1.454 |
| r_angle_other_deg | 1.358 |
| r_chiral_restr | 0.074 |
| r_bond_refined_d | 0.01 |
| r_bond_other_d | 0.006 |
| r_gen_planes_refined | 0.006 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 8165 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 9 |
| Heterogen Atoms | 6 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| xia2 | data reduction |
| xia2 | data scaling |
| PHENIX | phasing |
