2XZP
Upf1 helicase
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
---|---|---|---|---|
ID | Method | pH | Temperature | Details |
1 | 6 | 50MM SODIUM CITRATE PH 6.0, 1.5M SODIUM MALONATE |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.73 | 67.05 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 146.12 | α = 90 |
b = 146.12 | β = 90 |
c = 146.12 | γ = 90 |
Symmetry | |
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Space Group | P 21 3 |
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 PILATUS 6M | LN2-COOLED DYNAMICALLY BENDABLE MIRROR | 2010-06-25 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06SA | SLS | X06SA |
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 | 2.72 | 84.36 | 99.8 | 0.06 | 32.2 | 13.4 | 28118 | 4.4 | 66.66 |
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 | 2.72 | 2.87 | 98.7 | 0.64 | 4.4 | 13.6 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution 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 | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | PDB ENTRY 2WJV | 2.72 | 84.362 | 2.06 | 28090 | 1405 | 99.79 | 0.1751 | 0.1731 | 0.2141 | 62.5 |
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 | 13.27 |
f_angle_d | 0.785 |
f_chiral_restr | 0.056 |
f_bond_d | 0.009 |
f_plane_restr | 0.003 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4728 |
Nucleic Acid Atoms | |
Solvent Atoms | 38 |
Heterogen Atoms | 32 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
SCALA | data scaling |
PHASER | phasing |