X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3SE6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529710% PEG 8000, 20% ethylene glycol, 61 mM MES, 39 mM imidazole, 20 mM sodium-L-glutamate, 20 mM D-L-alanine, 20 mM glycine, 20 mM D-L-lysine, 20 mM D-L-serine (Morpheus H2)
Crystal Properties
Matthews coefficientSolvent content
3.1961.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.233α = 90
b = 135.453β = 90.11
c = 127.283γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2016-07-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.97931APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.4529.89597.20.087310.0710.0970.050.99611.93.89090654.25
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.4512.5899.71.0441.0441.3550.6870.83.8

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-VALUE3SE62.4529.291.3390736202797.060.20870.2080.236182.35
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_d11.7687
f_angle_d0.487
f_chiral_restr0.0396
f_plane_restr0.0031
f_bond_d0.0018
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14209
Nucleic Acid Atoms
Solvent Atoms209
Heterogen Atoms560

Software

Software
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing