5V2Y

Ethylene forming enzyme in complex with manganese, 2-oxoglutarate and L-arginine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5V2T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5277.150.2 ul 64 mg/ml EFE (+4 mM manganese chloride, 25 mM HEPES pH 8.0, 1 mM TCEP, 2.5 mM 2-oxoglutarate, 2.5 mM L-arginine) was mixed with 0.2 ul reservoir solution. The sitting drop reservoir of 50 ul contained 0.2 M sodium chloride, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350. The crystal was soaked for about a minute in 25% w/v Polyethylene glycol 400, 75% reservoir solution before freezing it.
Crystal Properties
Matthews coefficientSolvent content
2.1943.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.479α = 90
b = 82.116β = 90
c = 87.593γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.9786APS21-ID-G

Data Collection

Overall
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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.42843.899.70.0650.0720.0290.99915.95.86541012.11
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)RedundancyNumber Unique Reflections (All)
11.431.4596.30.6020.6950.3410.7733.93159

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE5V2T1.42843.7971.9162374323499.60.13340.1320.160718.4836
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
KeyRefinement Restraint Deviation
f_dihedral_angle_d14.864
f_angle_d0.949
f_chiral_restr0.075
f_bond_d0.007
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2715
Nucleic Acid Atoms
Solvent Atoms353
Heterogen Atoms42

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction