5FT9
Arabidopsis thaliana nuclear protein-only RNase P 2 (PRORP2)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | MICROBATCH | 6 | 277 | PRORP2 STOCK SOLUTION WAS PREPARED AT 2.5 MG/ML IN 50 MM HEPES-NA PH 7.5, 250 MM NACL, 5%(W/V) GLYCEROL, 1 MM TCEP. PRORP2 WAS CRYSTALLIZED AT 277 K IN 2 MICROLITER MICROBATCH DROPS SET UP UNDER PARAFIN OIL BY MIXING 1 VOLUME OF PRORP2 SOLUTION WITH 1 VOLUME OF CRYSTALLANT SOLUTION CONTAINING 200 MM SODIUM MALONATE PH 6, 20% (W/V) PEG 3350. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.4 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 70.5 | α = 63.1 |
b = 72.8 | β = 72.2 |
c = 80.3 | γ = 78.4 |
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 2M | 2013-02-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SLS BEAMLINE X06DA | SLS | X06DA |
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 | 3.05 | 35 | 92.4 | 0.12 | 8.7 | 3.5 | 23923 | -3 | 93.61 |
Highest Resolution Shell | |||||||||||||||||||
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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 | 3.05 | 3.23 | 98.2 | 1.5 | 0.8 | 3.7 |
Refinement
Statistics | |||||||||||||||||||
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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 4G26 | 3.05 | 34.707 | 1.91 | 23727 | 1126 | 92.2 | 0.2444 | 0.2421 | 0.2897 | 145.9 |
Temperature Factor Modeling | ||||||
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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 | 15.092 |
f_angle_d | 1.148 |
f_chiral_restr | 0.051 |
f_bond_d | 0.005 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 7442 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms | 2 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |