3ABT

Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DW4PDB ENTRY 2DW4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52783-10% PEG 2000 Monomethyl ether, 0.1M Hepes pH 7.5, 0.2M magnesium chloride, 0.1M cacodylate, 5mM Tranylcypromine-derivative, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties
Matthews coefficientSolvent content
3.6165.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 183.84α = 90
b = 183.84β = 90
c = 109.15γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-04-15MSINGLE WAVELENGTH
21x-ray100CCDMARMOSAIC 225 mm CCD2008-12-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.000000SPring-8BL41XU
2SYNCHROTRONSPRING-8 BEAMLINE BL26B21.000000SPring-8BL26B2

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
1,23.250990.2269.778.718396
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
3.213.3498.20.6120.6122.114.42820

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DW43.247.732.11839689399.80.2310.2310.272RANDOM58.9
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]
9.789.78-19.57
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.9
c_mcangle_it1.07
c_angle_deg0.9
c_scangle_it0.86
c_improper_angle_d0.7
c_mcbond_it0.57
c_scbond_it0.47
c_bond_d0.003
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d20.9
c_mcangle_it1.07
c_angle_deg0.9
c_scangle_it0.86
c_improper_angle_d0.7
c_mcbond_it0.57
c_scbond_it0.47
c_bond_d0.003
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5049
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms68

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling