4J2N
Crystal Structure of mycobacteriophage Pukovnik Xis
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 300 | ammonium sulfate, PEG 3350, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 300K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
4.19 | 70.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 89.423 | α = 90 |
b = 129.985 | β = 90 |
c = 92.346 | γ = 90 |
Symmetry | |
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Space Group | C 2 2 21 |
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 | RIGAKU SATURN 944 | 2009-07-15 | M | SINGLE WAVELENGTH | ||||||
2 | 1 | x-ray | 100 | CCD | ADSC QUANTUM 4 | 2009-10-02 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU FR-E DW | 1.5418 | ||
2 | SYNCHROTRON | NSLS BEAMLINE X25 | 0.97910 | NSLS | X25 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (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 | 2.35 | 90 | 99.8 | 22860 | 22815 | 3 | 2 | 45.18 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.35 | 2.39 | 100 | 2.2 | 4.2 | 1127 |
Refinement
Statistics | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction ID | Structure Solution Method | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | SAD | 2.348 | 35.921 | 0.03 | 22795 | 20286 | 1788 | 88.8 | 0.264 | 0.2294 | 0.2257 | 0.267 | RANDOM | 54.6141 |
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] | |
24.4775 | -8.6062 | -15.8713 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.174 |
f_angle_d | 0.984 |
f_chiral_restr | 0.055 |
f_bond_d | 0.007 |
f_plane_restr | 0.005 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 2113 |
Nucleic Acid Atoms | |
Solvent Atoms | 140 |
Heterogen Atoms | 40 |
Software
Software | |
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Software Name | Purpose |
PHENIX | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
DENZO | data reduction |
SCALEPACK | data scaling |
PHENIX | phasing |