3ZN4
VP16, a capsid protein of bacteriophage P23-77 (VP16-type-2)
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3ZMO | PDB ENTRY 3ZMO |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4 | SITTING DROP VAPOUR DIFFUSION SYSTEM IN A 96-WELL PLATE, 200 NL OF PROTEIN (2-3 MG/ML IN 20 MM TRIS-BUFFER PH 7.4) MIXED WITH 200 NL SOLUTION CONSISTING 20%(W/V) PEG6000 AND 0.1 M CITRATE PH 4. |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.15 | 39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 76.6 | α = 90 |
b = 68.57 | β = 96.44 |
c = 31.58 | γ = 90 |
Symmetry | |
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Space Group | C 1 2 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 | CCD | ADSC CCD | 2010-06-26 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I04 | Diamond | I04 |
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 | 1.26 | 34.3 | 85.8 | 0.05 | 23.1 | 7.5 | 37146 | 10.67 |
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 | 1.26 | 1.3 | 41.4 | 0.63 | 2.6 | 6.5 |
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 3ZMO | 1.26 | 17.79 | 37133 | 1855 | 84.96 | 0.1577 | 0.1563 | 0.184 | RANDOM | 16.06 |
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] | |
-1.1331 | -0.983 | 0.3885 | 0.7446 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
t_other_torsion | 12.68 |
t_omega_torsion | 4.41 |
t_angle_deg | 1.08 |
t_bond_d | 0.01 |
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 | 1167 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 14 |
Software
Software | |
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Software Name | Purpose |
BUSTER | refinement |
xia2 | data reduction |
xia2 | data scaling |
PHASER | phasing |