2VFO
Low Temperature Structure of P22 Tailspike Protein Fragment (109-666), Mutant V125L
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1TYV | PDB ENTRY 1TYV |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | 10 | DROP: 2 MICROLITER 1.5 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0, PLUS 3.3 MICROLITER 10 MG/ML PROTEIN SOLUTION IN 10 MM HEPES, PH 7.0; RESERVOIR: 750 MICOLITER 1.0 M AMMONIUM SULFATE, 0.1 M SODIUM PHOSPHATE, PH 10.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.42 | 49.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 120.27 | α = 90 |
b = 120.27 | β = 90 |
c = 120.27 | γ = 90 |
Symmetry | |
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Space Group | P 21 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 | CCD | MARRESEARCH | MIRRORS | 2006-10-29 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | BESSY | 14.1 |
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 | 1.59 | 50 | 98.1 | 0.04 | 32.2 | 9.3 | 76307 | 16.5 |
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 | 1.59 | 1.7 | 90.6 | 0.1 | 8.9 | 2.5 |
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 1TYV | 1.5 | 30 | 78569 | 4158 | 88.9 | 0.123 | 0.122 | 0.144 | RANDOM | 10.29 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 35.509 |
r_dihedral_angle_4_deg | 15.807 |
r_dihedral_angle_3_deg | 11.174 |
r_dihedral_angle_1_deg | 6.689 |
r_scangle_it | 4.354 |
r_scbond_it | 3.027 |
r_mcangle_it | 2.021 |
r_mcbond_it | 1.48 |
r_angle_refined_deg | 1.263 |
r_angle_other_deg | 0.86 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4207 |
Nucleic Acid Atoms | |
Solvent Atoms | 796 |
Heterogen Atoms | 48 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
PHASER | phasing |