6YKF
VcaM4I restriction endonuclease in the presence of 5mC-modified ssDNA
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 5.25 | 291 | RESERVOIR SOLUTION: 1.6 M (NH4)2SO4 , 0.1 M MES PH 5.25; PROTEIN:DNA SOLUTION: 0.3 M NACL, 15 MM TRIS-HCL PH 8.5 AND 1 MM TCEP. FOR CRYO-PROTECTION THE RESERVOIR SOLUTION WAS DILUTED WITH GLYCEROL TO ACHIEVE 30% CONCENTRATION. |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.61 | 65.93 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 129 | α = 90 |
| b = 129 | β = 90 |
| c = 110.911 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 62 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 PILATUS 6M-F | 2019-12-15 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1) | 0.97626 | PETRA III, EMBL c/o DESY | P13 (MX1) |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 1.48 | 42.23 | 98.9 | 0.091 | 0.096 | 0.999 | 14.95 | 10.6 | 90208 | 26.7 | |||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.48 | 1.56 | 98.5 | 0.967 | 1.019 | 0.742 | 1.91 | 10.1 | |||||||||||
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 | 6YJB | 1.48 | 42.23 | 85724 | 4481 | 98.87 | 0.1702 | 0.1693 | 0.1881 | RANDOM | 23.433 | ||||||
| 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] | |
| 0.72 | 0.36 | 0.72 | -2.34 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 34.11 |
| r_dihedral_angle_4_deg | 20.085 |
| r_dihedral_angle_3_deg | 13.63 |
| r_dihedral_angle_1_deg | 6.436 |
| r_angle_other_deg | 1.384 |
| r_angle_refined_deg | 1.288 |
| r_chiral_restr | 0.065 |
| r_bond_refined_d | 0.006 |
| r_gen_planes_refined | 0.006 |
| r_gen_planes_other | 0.002 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2499 |
| Nucleic Acid Atoms | 100 |
| Solvent Atoms | 589 |
| Heterogen Atoms | 121 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| XDS | data reduction |
| XDS | data scaling |
| PDB_EXTRACT | data extraction |
| REFMAC | phasing |
