6IE3
Crystal structure of methyladenine demethylase
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 286 | 5% ethanol, 5% MPD, 100 mM NaF, 100 mM HepespH7.5 |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 2.03 | 39.35 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 56.732 | α = 90 |
| b = 56.732 | β = 90 |
| c = 191.686 | γ = 120 |
| Symmetry | |
|---|---|
| Space Group | P 65 |
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 | 2017-01-30 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | SSRF BEAMLINE BL19U1 | 0.97929 | SSRF | BL19U1 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | 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 | 1.97 | 50 | 99.4 | 0.095 | 0.099 | 0.026 | 23.1 | 15.3 | 24558 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
| 1 | 1.97 | 2 | 0.746 | 0.783 | 0.232 | ||||||||||||||
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 | 1.97 | 49.13 | 20188 | 978 | 86.11 | 0.20398 | 0.20253 | 0.22 | 0.2331 | 0.24 | RANDOM | 31.318 | |||||
| Temperature Factor Modeling | ||||||
|---|---|---|---|---|---|---|
| Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[2][2] | Anisotropic B[3][3] | |||
| 0.15 | 0.07 | 0.15 | -0.48 | |||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.978 |
| r_dihedral_angle_3_deg | 13.717 |
| r_dihedral_angle_4_deg | 11.97 |
| r_dihedral_angle_1_deg | 6.011 |
| r_long_range_B_refined | 5.336 |
| r_long_range_B_other | 5.174 |
| r_mcangle_it | 2.769 |
| r_mcangle_other | 2.768 |
| r_scangle_other | 2.123 |
| r_mcbond_it | 1.547 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 2419 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 283 |
| Heterogen Atoms | 4 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-3000 | data scaling |
| AutoSol | phasing |
| ARP/wARP | model building |
