7C0L
Crystal structure of a dinucleotide-binding protein of ABC transporter endogenously bound to uridylyl-3'-5'-phospho-guanosine (Form III)
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 6.5 | 277 | 0.2M ammonium phosphate, 0.1M sodium cacodylate pH6.5, 30% PEG 8000 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.22 | 44.53 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 65.91 | α = 90 |
b = 58.12 | β = 93.04 |
c = 102.4 | 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 | IMAGE PLATE | RIGAKU RAXIS IV++ | VariMax HF | 2016-05-20 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | ROTATING ANODE | RIGAKU MICROMAX-007 HF | 1.5418 |
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 | 1.85 | 56.79 | 83.8 | 0.125 | 0.152 | 0.086 | 0.978 | 9.3 | 2.8 | 55937 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 | 1.85 | 1.89 | 82.3 | 0.425 | 0.527 | 0.307 | 0.768 | 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 | 7C0F | 1.85 | 56.79 | 53158 | 2757 | 83.87 | 0.1802 | 0.178 | 0.2227 | RANDOM | 18.671 |
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] | |
-1.36 | -0.04 | -0.7 | 2.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.192 |
r_dihedral_angle_4_deg | 21.829 |
r_dihedral_angle_3_deg | 14.52 |
r_dihedral_angle_1_deg | 6.284 |
r_angle_refined_deg | 1.882 |
r_angle_other_deg | 1.49 |
r_chiral_restr | 0.096 |
r_bond_refined_d | 0.014 |
r_gen_planes_refined | 0.011 |
r_bond_other_d | 0.001 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6072 |
Nucleic Acid Atoms | |
Solvent Atoms | 520 |
Heterogen Atoms | 139 |
Software
Software | |
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Software Name | Purpose |
HKL-3000 | data collection |
MOSFLM | data reduction |
Aimless | data scaling |
PHASER | phasing |
Coot | model building |
REFMAC | refinement |
PDB_EXTRACT | data extraction |