4DKW
Structure of P22 Large terminase nuclease domain
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 2WBN | PDB ENTRY 2WBN |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6 | 298 | 0.2 M magnesium sulfate, 20% w/v PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.63 | 53.2 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 60.921 | α = 90 |
b = 139.795 | β = 95.1 |
c = 61.005 | γ = 90 |
Symmetry | |
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Space Group | P 1 21 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 QUANTUM 270 | 2011-09-01 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | NSLS BEAMLINE X6A | 0.972 | NSLS | X6A |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (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 | 2.02 | 15 | 90.8 | 0.078 | 0.078 | 18.4 | 60520 | 1 | 1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.02 | 2.09 | 54.9 | 0.61 | 0.61 | 2.2 | 1.9 | 3673 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Starting model | Resolution (High) | Resolution (Low) | Cut-off Sigma (F) | 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 | PDB ENTRY 2WBN | 2.02 | 14.968 | 1.34 | 60494 | 2250 | 81.68 | 0.1672 | 0.1656 | 0.197 | thin shells resolution |
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] | |
-4.9997 | 0.1305 | -1.9809 | 6.9805 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
f_dihedral_angle_d | 14.675 |
f_angle_d | 1.097 |
f_chiral_restr | 0.08 |
f_bond_d | 0.01 |
f_plane_restr | 0.004 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6376 |
Nucleic Acid Atoms | |
Solvent Atoms | 1112 |
Heterogen Atoms | 28 |
Software
Software | |
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Software Name | Purpose |
HKL-2000 | data collection |
PHASER | phasing |
PHENIX | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |