3NF4

Crystal structure of acyl-CoA dehydrogenase from Mycobacterium thermoresistibile bound to flavin adenine dinucleotide


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DVL2dvl molecule a

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP528969.7 mg/mL protein against PACT screen condition e11, 0.2 M Na Citrate, 20% PEG 3350 with 20% ethylene glycol as cryo-protectant, crystal tracking ID 215726e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4449.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.65α = 90
b = 99.23β = 90
c = 171.49γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2010-05-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.21.0ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.355098.80.06322.18.63438433958-344.057
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.4196.90.3396.68.82504

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2dvl molecule a2.3519.6933892169798.570.1940.1910.24RANDOM59.617
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]
-3.08-0.353.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.436
r_dihedral_angle_4_deg16.537
r_dihedral_angle_3_deg16.414
r_dihedral_angle_1_deg5.445
r_scangle_it3.324
r_scbond_it2.047
r_angle_refined_deg1.453
r_mcangle_it1.219
r_mcbond_it0.639
r_chiral_restr0.096
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.436
r_dihedral_angle_4_deg16.537
r_dihedral_angle_3_deg16.414
r_dihedral_angle_1_deg5.445
r_scangle_it3.324
r_scbond_it2.047
r_angle_refined_deg1.453
r_mcangle_it1.219
r_mcbond_it0.639
r_chiral_restr0.096
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5447
Nucleic Acid Atoms
Solvent Atoms169
Heterogen Atoms54

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction