3B78
Structure of the eEF2-ExoA(R551H)-NAD+ complex
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 7.2 | 293 | 7% PEG-10000, 3.5mM MPD, 100 mM HEPES, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.97 | 58.64 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 327.136 | α = 90 |
b = 68.128 | β = 102.994 |
c = 190.577 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | ADSC QUANTUM 315 | Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror, beam defining slits | 2007-03-17 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 1.0332 | APS | 19-ID |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | 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 | 2.5 | 50 | 93.1 | 0.176 | 6.7 | 3.5 | 144422 | 134457 | 48 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
2.5 | 2.59 | 72.1 | 0.505 | 1.3 | 1.9 | 10308 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | THROUGHOUT | 2.5 | 46.55 | 142482 | 132950 | 2810 | 93.31 | 0.206 | 0.206 | 0.206 | 0.242 | Test set chosen from eEF2-ExoA(E546H)-NAD+ | 71.95 |
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] | |
-3.216 | -0.43 | 8.636 | -5.42 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 15.174 |
f_nbd_refined | 4.124 |
f_angle_d | 0.591 |
f_chiral_restr | 0.039 |
f_bond_d | 0.002 |
f_plane_restr | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 23986 |
Nucleic Acid Atoms | |
Solvent Atoms | 498 |
Heterogen Atoms | 132 |
Software
Software | |
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Software Name | Purpose |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
MOLREP | phasing |