3SLF
Crystal structure of BA2930 in complex with AcCoA and uracil
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 3IJW | PDB entry 3IJW |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 7.5 | 293 | 0.1M HEPES, 17% w/v PEG3350, 0.1M MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.21 | 44.45 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 36.716 | α = 90 |
b = 109.996 | β = 90 |
c = 133.072 | γ = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
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 | beryllium lenses | 2010-03-19 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | APS BEAMLINE 21-ID-F | 0.9787 | APS | 21-ID-F |
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 | 2.05 | 50 | 99.4 | 0.124 | 0.124 | 19.4 | 6.5 | 34755 | 34755 | -3 |
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 | 2.05 | 2.09 | 93.8 | 0.555 | 0.555 | 2.1 | 3.8 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | 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 | FOURIER SYNTHESIS | THROUGHOUT | PDB entry 3IJW | 2.05 | 50 | 32867 | 32867 | 1733 | 99.39 | 0.19237 | 0.18966 | 0.24547 | RANDOM | 31.499 |
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] | |
0.01 | -0.54 | 0.53 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 37.582 |
r_dihedral_angle_4_deg | 18.643 |
r_dihedral_angle_3_deg | 14.785 |
r_dihedral_angle_1_deg | 6.12 |
r_scangle_it | 3.31 |
r_scbond_it | 2.207 |
r_angle_refined_deg | 1.341 |
r_mcangle_it | 1.069 |
r_angle_other_deg | 0.859 |
r_mcbond_it | 0.55 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4087 |
Nucleic Acid Atoms | |
Solvent Atoms | 255 |
Heterogen Atoms | 115 |
Software
Software | |
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Software Name | Purpose |
MD2 | data collection |
HKL-3000 | phasing |
MOLREP | phasing |
REFMAC | refinement |
Coot | model building |
HKL-3000 | data reduction |
HKL-3000 | data scaling |