Crystal structure of PvuRts1I, a 5-hydroxymethylcytosine DNA restriction endonuclease
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, SITTING DROP | 10.5 | 286 | 1.128M NaH2PO4, 0.752M K2HPO4, 0.1M CAPS pH 10.5, 0.19M Li2SO4, 6%(v/v) glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 286K |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 4.19 | 70.67 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 160.21 | α = 90 |
| b = 160.21 | β = 90 |
| c = 45.12 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 43 21 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 | CCD | MARMOSAIC 225 mm CCD | 2013-03-25 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL17U | 0.9791 | SSRF | BL17U |
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 | 2.9 | 56.71 | 98.1 | 0.12 | 12.9 | 10.5 | 13568 | 13311 | 12.9 | 12.9 | |||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work (Depositor) | R-Work (DCC) | R-Free (Depositor) | R-Free (DCC) | R-Free Selection Details | Mean Isotropic B | |||||
| X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.9 | 56.71 | 12620 | 662 | 97.63 | 0.25373 | 0.25202 | 0.2629 | 0.28695 | 0.2913 | RANDOM | 55.258 | |||||
| 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] | |
| -0.95 | -0.95 | 1.9 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 36.111 |
| r_dihedral_angle_4_deg | 25.153 |
| r_dihedral_angle_3_deg | 24.478 |
| r_dihedral_angle_1_deg | 7.484 |
| r_long_range_B_other | 5.474 |
| r_long_range_B_refined | 5.473 |
| r_mcangle_it | 5.264 |
| r_scangle_other | 5.135 |
| r_scbond_other | 4.06 |
| r_mcangle_other | 3.946 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2184 |
| Nucleic Acid Atoms | |
| Solvent Atoms | |
| Heterogen Atoms | |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| HKL-2000 | data collection |
| PHENIX | model building |
| REFMAC | refinement |
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHENIX | phasing |
