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Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 19
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BAY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 297 Sodium Tartrate 1.2 M as precipitant in Sodium Citrate buffer pH 5.6
Crystal Properties Matthews coefficient Solvent content 80
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.51 α = 90 b = 180.44 β = 90 c = 235.42 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 2013-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 1.0 ESRF ID14-2
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 80 99.4 0.151 0.993 4.3 4.1 42318
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 99.4 0.993 0.37 0.7 3.9
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 4BAY 3.2 80 40986 811 97.76 0.19379 0.19321 0.2006 0.22017 0.2256 RANDOM 114.712
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.677 r_dihedral_angle_4_deg 19.862 r_dihedral_angle_3_deg 18.815 r_long_range_B_refined 14.921 r_long_range_B_other 14.921 r_scangle_other 11.14 r_mcangle_it 10.419 r_mcangle_other 10.418 r_scbond_it 6.723 r_scbond_other 6.722
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.677 r_dihedral_angle_4_deg 19.862 r_dihedral_angle_3_deg 18.815 r_long_range_B_refined 14.921 r_long_range_B_other 14.921 r_scangle_other 11.14 r_mcangle_it 10.419 r_mcangle_other 10.418 r_scbond_it 6.723 r_scbond_other 6.722 r_mcbond_it 6.647 r_mcbond_other 6.646 r_dihedral_angle_1_deg 6.423 r_angle_refined_deg 1.341 r_angle_other_deg 0.768 r_chiral_restr 0.064 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 6325 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 74
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction Aimless data scaling REFMAC phasing