3RHF
Crystal structure of Polyphosphate Kinase 2 from Arthrobacter aurescens TC1
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 289 | 0.1 M Phosphate Citrate, 40% PEG 300, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.07 | 60 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 126.353 | α = 90 |
b = 126.353 | β = 90 |
c = 199.064 | γ = 90 |
Symmetry | |
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Space Group | P 41 21 2 |
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 315r | mirror | 2011-04-05 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 19-ID | 0.9794 | APS | 19-ID |
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 | 2.45 | 40 | 100 | 0.153 | 15 | 6.4 | 59938 | 59938 | 2 | 2 | 47.6 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||||
1 | 2.45 | 2.49 | 100 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Resolution (High) | Resolution (Low) | Cut-off Sigma (I) | Cut-off Sigma (F) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||
X-RAY DIFFRACTION | SAD | THROUGHOUT | 2.45 | 40 | 2 | 2 | 59634 | 56629 | 3005 | 99.5 | 0.19 | 0.18685 | 0.18429 | 0.235 | RANDOM | 27.39 |
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] | |
0.64 | 0.64 | -1.28 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.84 |
r_dihedral_angle_4_deg | 18.055 |
r_dihedral_angle_3_deg | 16.768 |
r_dihedral_angle_1_deg | 6.246 |
r_scangle_it | 4.435 |
r_scbond_it | 2.755 |
r_angle_refined_deg | 1.778 |
r_mcangle_it | 1.583 |
r_angle_other_deg | 1.11 |
r_mcbond_it | 0.809 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 8770 |
Nucleic Acid Atoms | |
Solvent Atoms | 461 |
Heterogen Atoms | 193 |
Software
Software | |
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Software Name | Purpose |
SBC-Collect | data collection |
HKL-3000 | phasing |
PHENIX | model building |
SHELX | model building |
ARP/wARP | model building |
MLPHARE | phasing |
REFMAC | refinement |
HKL-3000 | data reduction |
HKL-3000 | data scaling |
PHENIX | phasing |
SHELX | phasing |