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Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 15
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2V1D
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 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 coefficient Solvent content 6.22 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.07 α = 90 b = 178.69 β = 90 c = 235.61 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARRESEARCH 2013-10-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 1.00004 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 57.75 99.6 0.136 0.992 9.2 3.8 50761
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) Redundancy Number Unique Reflections (All) 1 3 3.1 99.9 0.96 0.382 1.1 4.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 2V1D 3 57.7 48697 967 97.14 0.21204 0.21168 0.2194 0.2296 0.2377 RANDOM 85.793
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] 8.32 -4.16 -4.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.284 r_dihedral_angle_3_deg 20.581 r_dihedral_angle_4_deg 18.865 r_long_range_B_refined 10.215 r_long_range_B_other 10.214 r_mcangle_it 7.149 r_mcangle_other 7.149 r_scangle_other 7.126 r_dihedral_angle_1_deg 6.07 r_mcbond_it 4.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.284 r_dihedral_angle_3_deg 20.581 r_dihedral_angle_4_deg 18.865 r_long_range_B_refined 10.215 r_long_range_B_other 10.214 r_mcangle_it 7.149 r_mcangle_other 7.149 r_scangle_other 7.126 r_dihedral_angle_1_deg 6.07 r_mcbond_it 4.47 r_mcbond_other 4.468 r_scbond_it 4.321 r_scbond_other 4.32 r_angle_refined_deg 1.381 r_angle_other_deg 0.822 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 6290 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing