6R2C
Crystal structure of the SucA domain of Mycobacterium smegmatis KGD after soaking with succinylphosphonate phosphonoethyl ester (PESP)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7 | 277 | 60% MPD, 22.5 mM Na acetate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.69 | 54.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 81.39 | α = 99.54 |
b = 83.96 | β = 98.78 |
c = 160.68 | γ = 100.89 |
Symmetry | |
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Space Group | P 1 |
Diffraction
Diffraction Experiment | ||||||||||||||
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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 | 2012-03-18 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.97895 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.09 | 78.48 | 97.4 | 0.07 | 0.048 | 0.997 | 10 | 2.9 | 233909 | 35.94 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 2.09 | 2.12 | 96.4 | 0.565 | 0.399 | 0.83 | 2.2 | 2.8 |
Refinement
Statistics | |||||||||||||||||||
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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 | FOURIER SYNTHESIS | THROUGHOUT | 2YIC | 2.09 | 21.07 | 233039 | 11680 | 97.4 | 0.233 | 0.232 | 0.246 | RANDOM | 43.36 |
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] | |
-10.374 | -3.3678 | 0.4197 | 3.3983 | 0.0538 | 6.9756 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_omega_torsion | 3 |
t_other_torsion | 2.63 |
t_angle_deg | 0.94 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 25237 |
Nucleic Acid Atoms | |
Solvent Atoms | 847 |
Heterogen Atoms | 164 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
XDS | data reduction |
autoPROC | data scaling |
REFMAC | phasing |