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Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 34
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 The 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 6.43 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.409 α = 90 b = 181.155 β = 90 c = 237.456 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 PIXEL DECTRIS PILATUS 300K 2014-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00004 SLS X06DA
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 3.2 50 99.4 0.096 0.997 12.9 5.2 43214
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 3.2 3.32 97.6 0.926 0.551 1.6 5.2
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 3.2 50 42378 835 99.17 0.18492 0.18446 0.1909 0.20649 0.2088 RANDOM 101.407
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.731 r_dihedral_angle_3_deg 20.568 r_dihedral_angle_4_deg 17.013 r_long_range_B_refined 12.375 r_long_range_B_other 12.374 r_scangle_other 8.632 r_mcangle_it 7.983 r_mcangle_other 7.982 r_dihedral_angle_1_deg 6.115 r_scbond_it 5.187
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.731 r_dihedral_angle_3_deg 20.568 r_dihedral_angle_4_deg 17.013 r_long_range_B_refined 12.375 r_long_range_B_other 12.374 r_scangle_other 8.632 r_mcangle_it 7.983 r_mcangle_other 7.982 r_dihedral_angle_1_deg 6.115 r_scbond_it 5.187 r_scbond_other 5.186 r_mcbond_it 5.085 r_mcbond_other 5.085 r_angle_refined_deg 1.359 r_angle_other_deg 0.782 r_chiral_restr 0.062 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 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 6293 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing