5LGU

Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 34


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V1D 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.5293The hanging-drop vapor diffusion method at 20 C by mixing equal volumes of 100 microM LSD1-CoREST solution in 5% (w/v) glycerol, 25 mm potassium phosphate, pH 7.2, with reservoir solutions containing 1.2 M sodium/potassium tartrate and 100 mmN-(2-acetamido)-2-iminodiacetic acid, pH 6.5.
Crystal Properties
Matthews coefficientSolvent content
6.4380

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 121.409α = 90
b = 181.155β = 90
c = 237.456γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 300K2014-04-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.00004SLSX06DA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
13.25099.40.0960.99712.95.243214
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.3297.60.9260.5511.65.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUT2V1D3.2504237883599.170.184920.184460.20649RANDOM101.407
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]
7.04-5.32-1.73
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.731
r_dihedral_angle_3_deg20.568
r_dihedral_angle_4_deg17.013
r_long_range_B_refined12.375
r_long_range_B_other12.374
r_scangle_other8.632
r_mcangle_it7.983
r_mcangle_other7.982
r_dihedral_angle_1_deg6.115
r_scbond_it5.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.731
r_dihedral_angle_3_deg20.568
r_dihedral_angle_4_deg17.013
r_long_range_B_refined12.375
r_long_range_B_other12.374
r_scangle_other8.632
r_mcangle_it7.983
r_mcangle_other7.982
r_dihedral_angle_1_deg6.115
r_scbond_it5.187
r_scbond_other5.186
r_mcbond_it5.085
r_mcbond_other5.085
r_angle_refined_deg1.359
r_angle_other_deg0.782
r_chiral_restr0.062
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6293
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms86

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing