4Z9D
EcPltA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 277 | Treated with 20 mM NAD+ for thirty minutes prior to crystallization, 1:1 protein to 4-7% PEG, 0.1 M Tris, pH 8.5, 0.15 M lithium sulfate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.3 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 44.52 | α = 90.06 |
b = 55.66 | β = 104.07 |
c = 73.06 | γ = 96.17 |
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 | CCD | ADSC QUANTUM 315r | 2013-10-30 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | AUSTRALIAN SYNCHROTRON BEAMLINE MX2 | 0.95370 | Australian Synchrotron | MX2 |
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 | 1.8 | 70.8 | 88.5 | 0.066 | 7.7 | 1.7 | 91849 | 55479 | 10.6 |
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) | |||||||||||
1 | 1.8 | 1.9 | 87.7 | 0.3 | 2.6 | 1.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | FREE R-VALUE | PDB entry 4Z9C | 1.8 | 35.894 | 1.97 | 55466 | 2818 | 88.5 | 0.1832 | 0.1809 | 0.2269 | 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 | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 16.385 |
f_angle_d | 1.179 |
f_chiral_restr | 0.052 |
f_bond_d | 0.007 |
f_plane_restr | 0.006 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 5569 |
Nucleic Acid Atoms | |
Solvent Atoms | 598 |
Heterogen Atoms | 178 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
iMOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |