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Crystal structure of LSD1-CoREST in complex with PRSFLVRRK peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5H6Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.72 α = 90 b = 180.23 β = 90 c = 232.235 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-F 2017-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.68 48.87 100 1 25.3 13.6 71799
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.68 2.74 0.724 1.5
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 5H6Q 2.68 45 70287 1505 99.96 0.21409 0.21352 0.2161 0.2406 0.2408 RANDOM 82.889
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] 6.65 -5.09 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.857 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_3_deg 14.279 r_long_range_B_refined 7.32 r_long_range_B_other 7.319 r_dihedral_angle_1_deg 5.134 r_mcangle_it 4.793 r_mcangle_other 4.793 r_scangle_other 4.544 r_mcbond_it 2.904
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.857 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_3_deg 14.279 r_long_range_B_refined 7.32 r_long_range_B_other 7.319 r_dihedral_angle_1_deg 5.134 r_mcangle_it 4.793 r_mcangle_other 4.793 r_scangle_other 4.544 r_mcbond_it 2.904 r_mcbond_other 2.902 r_scbond_it 2.645 r_scbond_other 2.644 r_angle_refined_deg 1.19 r_angle_other_deg 1.081 r_chiral_restr 0.037 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 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 6285 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 71
Software Software Software Name Purpose REFMAC refinement Aimless data scaling MOLREP phasing Coot model building