7XW8

Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer, FAD-adduct


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2Z5U 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52930.1 M imidazole-HCl (pH 6.5), 10% PEG 3350, 10% 2-methyl-2,4-pentanediol and 50 mM ammonium formate
Crystal Properties
Matthews coefficientSolvent content
3.6366.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 184.727α = 90
b = 184.727β = 90
c = 108.937γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2014-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 5.0.20.97645ALS5.0.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.28501000.1160.1190.0288.221.450185
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.321000.3390.92720.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2Z5U2.2844.40949937241399.4360.20.19810.229950.805
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]
1.2790.6391.279-4.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.168
r_dihedral_angle_4_deg17.992
r_dihedral_angle_3_deg16.817
r_lrange_it11.991
r_scangle_it10.504
r_scbond_it7.732
r_mcangle_it7.418
r_dihedral_angle_1_deg5.798
r_mcbond_it5.701
r_angle_refined_deg1.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.168
r_dihedral_angle_4_deg17.992
r_dihedral_angle_3_deg16.817
r_lrange_it11.991
r_scangle_it10.504
r_scbond_it7.732
r_mcangle_it7.418
r_dihedral_angle_1_deg5.798
r_mcbond_it5.701
r_angle_refined_deg1.132
r_nbtor_refined0.305
r_nbd_refined0.198
r_symmetry_nbd_refined0.15
r_symmetry_xyhbond_nbd_refined0.146
r_xyhbond_nbd_refined0.13
r_chiral_restr0.085
r_gen_planes_refined0.005
r_bond_refined_d0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5012
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms79

Software

Software
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction