2YIB
Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2YI9 | PDB ENTRY 2YI9 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | CRYSTALS OF FULL-LENGTH VP1 WERE GROWN IN SITTING DROPS CONTAINING 100 NL PROTEIN (5.3 MG/ML) PLUS 5 MM MNCL2 AND 100 NL RESERVOIR SOLUTION (20% W/V PEG3350, 0.1 M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM CITRATE, 20 MM ATP, 5% V/V MPD, 10 MM NAOH) EQUILIBRATED AGAINST 95 UL RESERVOIRS AT 20.5 C. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.02 | 63.66 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 119.74 | α = 90 |
b = 195.45 | β = 90 |
c = 197.38 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 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 | ADSC QUANTUM 4r | 2006-12-16 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | ESRF BEAMLINE ID14-2 | ESRF | ID14-2 |
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 | 3.8 | 45.24 | 98.5 | 0.3 | 4.5 | 4.9 | 45508 | -3 | 51.01 |
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 | 3.8 | 4.01 | 99 | 0.82 | 1.8 | 4.7 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | 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 | THROUGHOUT | PDB ENTRY 2YI9 | 3.8 | 44.43 | 45473 | 2307 | 0.1858 | 0.1843 | 0.2129 | RANDOM | 99.51 |
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] | |
1.9344 | 6.3521 | -8.2865 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 16.68 |
t_omega_torsion | 2.49 |
t_angle_deg | 1.08 |
t_bond_d | 0.009 |
t_dihedral_angle_d | |
t_incorr_chiral_ct | |
t_pseud_angle | |
t_trig_c_planes | |
t_gen_planes | |
t_it |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 24183 |
Nucleic Acid Atoms | |
Solvent Atoms | |
Heterogen Atoms |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
MOSFLM | data reduction |
SCALA | data scaling |
PHASER | phasing |