2VBM
Tailspike protein of bacteriophage Sf6 complexed with tetrasaccharide
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2VBK | PDB ENTRY 2VBK |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 293 | VAPOR DIFFUSION HANGING DROP, 20 DEGR. CELSIUS; DROP: 3 MICROL RESERVOIR AND 3 MICROL PROTEIN SOLUTION; RESERVOIR: 0.1M MES, PH6.5, 16% PEG8000, 20MM MNCL2; PROTEIN: 10MG/ML, 10MM NA-PHOSPHATE,PH7.0, OCTASACCHARIDE CONCENTRATION/PROTEIN CONCENTATION 10:1; CRYOCONDITION: 0.1M MES, PH6.5, 25% PEG8000, 20MM MNCL2, 15% ETHYLENGLYCOL |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.9 | 57.7 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 95.358 | α = 90 |
b = 95.358 | β = 90 |
c = 182.765 | γ = 120 |
Symmetry | |
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Space Group | H 3 |
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 | IMAGE PLATE | MARRESEARCH | MIRRORS | 2005-07-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.2 | BESSY | 14.2 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym 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 | 2 | 47.7 | 99.7 | 0.06 | 17.4 | 4.9 | 39641 | 17.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2 | 2.07 | 97.2 | 0.22 | 7 | 4 |
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 2VBK | 2 | 47.67 | 39641 | 2110 | 99.8 | 0.192 | 0.19 | 0.232 | RANDOM | 20.2 |
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] | |
0.36 | 0.18 | 0.36 | -0.54 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.978 |
r_dihedral_angle_4_deg | 12.96 |
r_dihedral_angle_3_deg | 12.676 |
r_dihedral_angle_1_deg | 6.767 |
r_scangle_it | 2.843 |
r_scbond_it | 2.086 |
r_angle_refined_deg | 1.362 |
r_mcangle_it | 1.108 |
r_mcbond_it | 0.826 |
r_angle_other_deg | 0.766 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 3821 |
Nucleic Acid Atoms | |
Solvent Atoms | 248 |
Heterogen Atoms | 58 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
AMoRE | phasing |