4XLH
Tailspike protein double mutant D339A/E372A of E. coli bacteriophage HK620
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 4XM3 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 298 | 0.1 M Tris-HCl, 3.5 M Sodium formate |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.14 | 42.39 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 73.975 | α = 90 |
b = 73.975 | β = 90 |
c = 174.328 | γ = 120 |
Symmetry | |
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Space Group | P 3 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 | RAYONIX MX-225 | mirrors | 2012-11-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | BESSY BEAMLINE 14.1 | 0.91841 | BESSY | 14.1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | 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 | 1.91 | 43.04 | 99.6 | 0.107 | 0.051 | 0.998 | 14.1 | 5.4 | 43960 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||
1 | 1.91 | 1.95 | 94 | 0.761 | 0.368 | 0.652 | 2.1 | 5.1 | 2752 |
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 | 4XM3 | 1.91 | 43.04 | 43960 | 2189 | 99.93 | 0.1601 | 0.1574 | 0.2104 | RANDOM | 23.005 |
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] | |
0.52 | 0.26 | 0.52 | -1.69 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 36.441 |
r_dihedral_angle_4_deg | 15.834 |
r_dihedral_angle_3_deg | 12.259 |
r_dihedral_angle_1_deg | 7.235 |
r_angle_refined_deg | 1.674 |
r_mcangle_it | 1.285 |
r_mcbond_other | 0.876 |
r_mcbond_it | 0.87 |
r_angle_other_deg | 0.853 |
r_chiral_restr | 0.104 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4540 |
Nucleic Acid Atoms | |
Solvent Atoms | 449 |
Heterogen Atoms | 24 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
ARP | model building |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
REFMAC | phasing |