6KKW
Crystal structure of the complex of phosphopantetheine adenylyl transferase from Acinetobacter baumannii with Dephospho Coenzyme at 3.2 A resolution.
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 6JOG |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.6 | 298 | 1M LITHIUM SULPHATE, 2M AMMONIUM SULPHATE, 0.1M SODIUM CITRATE, PH 5.6 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
5.64 | 78.21 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 215.539 | α = 90 |
b = 215.539 | β = 90 |
c = 215.539 | γ = 90 |
Symmetry | |
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Space Group | F 41 3 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 | MARMOSAIC 225 mm CCD | 2019-07-10 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | RRCAT INDUS-2 BEAMLINE PX-BL21 | 1 | RRCAT INDUS-2 | PX-BL21 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rrim 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 | 3.2 | 49.5 | 92.27 | 0.117 | 0.98 | 30.61 | 8.5 | 6957 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rrim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 3.2 | 3.28 | 0.7 | 0.92 | 5.02 | 13 |
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 (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | 6JOG | 3.202 | 49.497 | 6957 | 334 | 92.378 | 0.178 | 0.175 | 0.2327 | 76.279 |
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] | |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 29.545 |
r_dihedral_angle_4_deg | 23.835 |
r_dihedral_angle_3_deg | 20.833 |
r_lrange_other | 17.225 |
r_lrange_it | 17.222 |
r_scangle_it | 13.69 |
r_scangle_other | 13.683 |
r_mcangle_it | 11.489 |
r_mcangle_other | 11.485 |
r_scbond_it | 9.2 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 1305 |
Nucleic Acid Atoms | |
Solvent Atoms | 22 |
Heterogen Atoms | 45 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
XDS | data reduction |
XSCALE | data scaling |
MOLREP | phasing |