6QZZ
full length OphA V404E in complex with SAH
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details |
| 1 | VAPOR DIFFUSION, HANGING DROP | 289 | 0.3-0.4 M KSCN, 0.1 M Bicine pH 9, 1.8-2.3 M Sodium malonate | |
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content |
| 3.7 | 66.77 |
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) |
| a = 164.002 | α = 90 |
| b = 91.723 | β = 90 |
| c = 85.222 | γ = 90 |
| Symmetry | |
|---|---|
| Space Group | P 21 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 | PIXEL | DECTRIS PILATUS3 6M | 2018-04-14 | M | SINGLE WAVELENGTH | ||||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
| 1 | SYNCHROTRON | DIAMOND BEAMLINE I03 | 0.9686 | Diamond | I03 |
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 1.85 | 80.1 | 100 | 0.044 | 1 | 16.9 | 7.2 | 798741 | 110277 | ||||||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
| 1 | 1.85 | 1.88 | 98.4 | 0.766 | 0.621 | 2 | 7.3 | ||||||||||||
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 | 5N0O | 1.85 | 80.05 | 104622 | 5568 | 99.9 | 0.20731 | 0.20638 | 0.22462 | RANDOM | 50.04 | ||||||
| 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] | |
| 0.75 | -0.91 | 0.16 | ||||
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation |
| r_dihedral_angle_2_deg | 33.06 |
| r_dihedral_angle_4_deg | 16.221 |
| r_dihedral_angle_3_deg | 13.355 |
| r_long_range_B_refined | 9.723 |
| r_long_range_B_other | 9.723 |
| r_scangle_other | 7.929 |
| r_dihedral_angle_1_deg | 6.783 |
| r_scbond_it | 5.867 |
| r_scbond_other | 5.867 |
| r_mcangle_it | 5.382 |
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number |
| Protein Atoms | 6083 |
| Nucleic Acid Atoms | |
| Solvent Atoms | 326 |
| Heterogen Atoms | 52 |
Software
| Software | |
|---|---|
| Software Name | Purpose |
| REFMAC | refinement |
| DIALS | data reduction |
| DIALS | data scaling |
| PHASER | phasing |
