3PFD
Crystal structure of an Acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to reduced flavin adenine dinucleotide solved by combined iodide ion SAD MR
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 1JQI |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 4.2 | 289 | MythA00185bA1 PS00649 116 mg/mL grown against JCSG+ C1 0.2 M NaCl, 0.1 M phosphate citrate pH 4.2, 20% PEG 8000 and soaked for 20 minutes against 15% PEG 8000, 25% PEG 400, 1 M NaI, 0.1 M phosphate citrate pH 4.2, crystal tracking ID 216661c1-1MNaI, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.35 | 47.63 |
Crystal Data
Unit Cell | |
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Length ( Å ) | Angle ( ˚ ) |
a = 74.43 | α = 90 |
b = 114.55 | β = 92.13 |
c = 92.77 | 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 | CCD | RIGAKU SATURN 944 | 2010-10-08 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
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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) | 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 | 2.1 | 50 | 99.3 | 0.132 | 11.74 | 7.2 | 89991 | -3 | 24.921 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R Merge I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1 | 2.1 | 2.15 | 91.2 | 0.531 | 3.5 | 6.2 | 6704 |
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 | SAD WITH MR | THROUGHOUT | 1jqi | 2.1 | 50 | 89872 | 4507 | 99.18 | 0.171 | 0.1691 | 0.2068 | RANDOM | 21.3214 |
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] | |
-0.57 | -0.36 | -0.09 | 0.63 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 34.866 |
r_dihedral_angle_4_deg | 17.561 |
r_dihedral_angle_3_deg | 13.581 |
r_dihedral_angle_1_deg | 5.346 |
r_scangle_it | 3.262 |
r_scbond_it | 2.033 |
r_angle_refined_deg | 1.393 |
r_mcangle_it | 1.17 |
r_mcbond_it | 0.664 |
r_chiral_restr | 0.092 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 10870 |
Nucleic Acid Atoms | |
Solvent Atoms | 623 |
Heterogen Atoms | 321 |
Software
Software | |
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Software Name | Purpose |
XSCALE | data scaling |
PHASER | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
StructureStudio | data collection |
XDS | data reduction |