3P1G
Crystal Structure of the Xenotropic Murine Leukemia Virus-Related Virus (XMRV) RNase H Domain
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 4.7 | 291 | PEG 1500, Magnesium Chloride, Sodium Citrate, pH 4.7, Vapor Diffusion, Hanging Drop, temperature 291K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
1.97 | 37.68 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 37.53 | α = 90 |
b = 37.53 | β = 90 |
c = 100.72 | γ = 90 |
Symmetry | |
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Space Group | P 41 |
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 | CCD | NOIR-1 | 2010-09-24 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ALS BEAMLINE 4.2.2 | 1.0 | ALS | 4.2.2 |
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 | 1.5 | 37.53 | 99.9 | 0.098 | 7.8 | 6.77 | 22272 |
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 | 1.5 | 1.55 | 99.3 | 0.771 | 2.1 | 3.66 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | 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 | 1.5 | 37.53 | 21970 | 1122 | 98.8 | 0.163 | 0.161 | 0.182 | 28.24 |
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 | 12.1 |
f_angle_d | 0.995 |
f_chiral_restr | 0.064 |
f_bond_d | 0.006 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1206 |
Nucleic Acid Atoms | |
Solvent Atoms | 162 |
Heterogen Atoms | 1 |
Software
Software | |
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Software Name | Purpose |
d*TREK | data scaling |
PHASER | phasing |
PHENIX | refinement |
PDB_EXTRACT | data extraction |