X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2IW5 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6290The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT]
Crystal Properties
Matthews coefficientSolvent content
80

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.073α = 90
b = 178.411β = 90
c = 234.676γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD12.7 KeV energy range, focused beam size: 50uM x 50uM2014-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.80349.01899.50.03723.814.66256362270
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.8032.873296.812.5

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-VALUE2IW52.80349.0181.3562268200099.550.2020.20110.226862.8
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_d14.966
f_angle_d0.743
f_chiral_restr0.027
f_plane_restr0.004
f_bond_d0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6293
Nucleic Acid Atoms86
Solvent Atoms23
Heterogen Atoms84

Software

Software
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Cootmodel building