4UYO

Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ZE3PDB ENTRY 3ZE3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1LIPIDIC CUBIC PHASE5.62930.2 %(V/V) 2-METHYL-2, 4-PENTANEDIOL (MPD), 0.1 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE/HCL PH 5.6. CRYSTALLIZED USING THE IN MESO (LIPID CUBIC PHASE) METHOD AT 20 DEGREES CELCIUS WITH THE 7.9 MONOACYLGLYCEROL (7.9 MAG) AS THE HOSTING LIPID.CRYSTALLIZATION WAS SET UP BY INCUBATING 20 MICROLITERS OF LIPID CUBIC PHASE WITH 400 MICROLITERS OF PRECIPITANT SOLUTION IN COUPLED SYRINGES.
Crystal Properties
Matthews coefficientSolvent content
2.9358.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.3α = 90
b = 91.8β = 90
c = 141.7γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293PIXELCornell-SLAC Pixel Array Detector (CSPAD)2013-03-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1FREE ELECTRON LASERSLAC LCLS BEAMLINE CXI1.302SLAC LCLSCXI

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
12.1840.510019346654058-571.31
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.182.241000.443519

Refinement

Statistics
Diffraction IDStructure Solution 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 REPLACEMENTPDB ENTRY 3ZE32.1840.0131.3351797258399.640.2090.20760.236270.42
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_d13.963
f_angle_d0.949
f_chiral_restr0.057
f_bond_d0.008
f_plane_restr0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4637
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms221

Software

Software
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing