Ab initio crystal structure of Selenomethionine labelled Mycobacterium smegmatis Mfd
X-RAY DIFFRACTION
Crystallization
| Crystalization Experiments | ||||
|---|---|---|---|---|
| ID | Method | pH | Temperature | Details | 
| 1 | VAPOR DIFFUSION, HANGING DROP | 7.2 | 295 | 100mM HEPES sodium pH 7.2, 0.2M Na2So4, 20% PEG3350 | 
| Crystal Properties | |
|---|---|
| Matthews coefficient | Solvent content | 
| 2.61 | 52.85 | 
Crystal Data
| Unit Cell | |
|---|---|
| Length ( Å ) | Angle ( ˚ ) | 
| a = 82.71 | α = 90 | 
| b = 158.87 | β = 90 | 
| c = 207.94 | γ = 90 | 
| Symmetry | |
|---|---|
| Space Group | P 21 21 21 | 
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 EIGER X 9M | Cryogenically cooled channel cut crystal monochromator, a convex prefocussing mirror and a KirkpatrickBaez pair of focussing mirrors. | 2016-03-26 | M | MAD | |||||
| Radiation Source | |||||
|---|---|---|---|---|---|
| ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline | 
| 1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 2 | 0.979029, 0.979183, 0.972425 | SOLEIL | PROXIMA 2 | 
Data Collection
| Overall | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim 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 | 2.99 | 47.19 | 99 | 0.132 | 0.137 | 0.037 | 0.998 | 14.4 | 13.7 | 55718 | 1.9 | 82.66 | |||||||
| Highest Resolution Shell | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
| 1 | 2.99 | 3.1 | 92.43 | 1.137 | 1.181 | 0.313 | 0.757 | 13.64 | |||||||||||
Refinement
| Statistics | |||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | MAD | FREE R-VALUE | 2.989 | 47.188 | 1.36 | 55708 | 2787 | 98.98 | 0.2207 | 0.2182 | 0.22 | 0.2697 | 0.27 | Random selection | |||||
| 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] | |
| RMS Deviations | |
|---|---|
| Key | Refinement Restraint Deviation | 
| f_dihedral_angle_d | 9.406 | 
| f_angle_d | 0.576 | 
| f_chiral_restr | 0.042 | 
| f_plane_restr | 0.004 | 
| f_bond_d | 0.003 | 
| Non-Hydrogen Atoms Used in Refinement | |
|---|---|
| Non-Hydrogen Atoms | Number | 
| Protein Atoms | 16754 | 
| Nucleic Acid Atoms | |
| Solvent Atoms | 74 | 
| Heterogen Atoms | 25 | 
Software
| Software | |
|---|---|
| Software Name | Purpose | 
| PHENIX | refinement | 
| XDS | data reduction | 
| XSCALE | data scaling | 
| CRANK2 | phasing | 














