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Crystal structure of LSD1-CoREST in complex with peptide 13
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, HANGING DROP 5.5 293 0.1 M N-(2-Acetamido) iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate tetrahydrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.674 α = 90 b = 178.374 β = 90 c = 234.848 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 2M 2015-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.6 50 99.8 0.08 19.3 6.5 80965 -3
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 2.6 2.64 99.9 0.681 0.845 2.4 6.1
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 MOLECULAR REPLACEMENT THROUGHOUT 2V1D 2.6 50 76940 1533 99.77 0.21738 0.21711 0.2171 0.23102 0.2313 RANDOM 76.47
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] 5.59 -4.16 -1.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_3_deg 14.723 r_dihedral_angle_4_deg 13.313 r_long_range_B_refined 6.239 r_dihedral_angle_1_deg 4.642 r_mcangle_it 3.189 r_scbond_it 1.98 r_mcbond_it 1.855 r_angle_refined_deg 1.17 r_chiral_restr 0.067
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.069 r_dihedral_angle_3_deg 14.723 r_dihedral_angle_4_deg 13.313 r_long_range_B_refined 6.239 r_dihedral_angle_1_deg 4.642 r_mcangle_it 3.189 r_scbond_it 1.98 r_mcbond_it 1.855 r_angle_refined_deg 1.17 r_chiral_restr 0.067 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6289 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement HKL-2000 data processing MOLREP phasing