5V85

The crystal structure of the protein of DegV family COG1307 from Ruminococcus gnavus ATCC 29149 (alternative refinement of PDB 3JR7 with Vaccenic acid)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.2M SODIUM CHLORIDE, 0.1M PHOSPHATE-CITRATE, 10%PEG3000, PH 4.2
Crystal Properties
Matthews coefficientSolvent content
3.3663.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.899α = 90
b = 96.899β = 90
c = 159.921γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3THIS IS UNALTERED ORIGINAL DATA FROM ENTRY 3JR72008-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.97915APS19-BM

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
1283.9299.417.855.2587852

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.00329.8871.3358785297099.440.16990.16850.1977
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_d6.423
f_angle_d0.533
f_chiral_restr0.044
f_bond_d0.003
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4287
Nucleic Acid Atoms
Solvent Atoms609
Heterogen Atoms62

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing