5LGN

Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 19


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4BAY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION5.6297Sodium Tartrate 1.2 M as precipitant in Sodium Citrate buffer pH 5.6
Crystal Properties
Matthews coefficientSolvent content
80

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.51α = 90
b = 180.44β = 90
c = 235.42γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2013-01-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-21.0ESRFID14-2

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
13.28099.40.1510.9934.34.142318
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)
13.23.3299.40.9930.370.73.9

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 SYNTHESISTHROUGHOUT4BAY3.2804098681197.760.193790.193210.22017RANDOM114.712
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]
8.22-3.08-5.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.677
r_dihedral_angle_4_deg19.862
r_dihedral_angle_3_deg18.815
r_long_range_B_refined14.921
r_long_range_B_other14.921
r_scangle_other11.14
r_mcangle_it10.419
r_mcangle_other10.418
r_scbond_it6.723
r_scbond_other6.722
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.677
r_dihedral_angle_4_deg19.862
r_dihedral_angle_3_deg18.815
r_long_range_B_refined14.921
r_long_range_B_other14.921
r_scangle_other11.14
r_mcangle_it10.419
r_mcangle_other10.418
r_scbond_it6.723
r_scbond_other6.722
r_mcbond_it6.647
r_mcbond_other6.646
r_dihedral_angle_1_deg6.423
r_angle_refined_deg1.341
r_angle_other_deg0.768
r_chiral_restr0.064
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d0.002
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 Atoms6325
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
REFMACphasing