6FU7
ATP phosphoribosyltransferase (HisZG ATPPRT) from Psychrobacter arcticus in complex with PRATP
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 5M8H | 5M8H partial model |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 8.5 | 277 | 8mg mL-1 protein (in 20mM Tris pH7, 50mM KCl, 10mM MgCl2, 2mM DTT, 0.5mM histidine) mixed in 1:1 ratio with precipitant solution (11% PEG3350, 100mM bicine pH8.5, 150mM SrCl2, 150mM KBr, 2% 1,6-hexanediol) |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.53 | 51.32 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 101.82 | α = 90 |
b = 146.78 | β = 101.77 |
c = 94.46 | γ = 90 |
Symmetry | |
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Space Group | C 1 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 | PIXEL | DECTRIS PILATUS3 6M | 2017-04-27 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | DIAMOND BEAMLINE I24 | 0.9686 | Diamond | I24 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | 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 | 2.31 | 73.39 | 99.2 | 0.073 | 0.086 | 0.045 | 0.996 | 10.4 | 3.7 | 58950 | 54.3 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Rrim I (All) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||
1 | 2.31 | 2.37 | 99.8 | 0.835 | 0.973 | 0.494 | 0.541 | 1.6 | 3.8 |
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 | 5M8H partial model | 2.31 | 73.39 | 56018 | 2916 | 99.14 | 0.2134 | 0.2118 | 0.2425 | RANDOM | 78.717 |
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] | |
2.74 | 0.77 | 0.68 | -3.44 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 38.232 |
r_dihedral_angle_4_deg | 15.93 |
r_dihedral_angle_3_deg | 13.705 |
r_dihedral_angle_1_deg | 5.977 |
r_angle_refined_deg | 1.285 |
r_angle_other_deg | 0.925 |
r_chiral_restr | 0.073 |
r_bond_refined_d | 0.008 |
r_gen_planes_refined | 0.004 |
r_bond_other_d | 0.002 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 9073 |
Nucleic Acid Atoms | |
Solvent Atoms | 149 |
Heterogen Atoms | 100 |
Software
Software | |
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Software Name | Purpose |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |