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Crystal structure of LSD1-CoREST in complex with PRSFLVRRP 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 = 121.466 α = 90 b = 180.689 β = 90 c = 232.682 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 2.64 48.95 100 1 1.6 13.6 75279
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 2.64 2.69 0.652
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5H6Q 2.64 45 73773 1498 99.96 0.2111 0.21069 0.23145 0.2053 RANDOM 82.643
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] 6.95 -4.77 -2.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.086 r_dihedral_angle_4_deg 15.51 r_dihedral_angle_3_deg 14.914 r_long_range_B_other 7.14 r_long_range_B_refined 7.138 r_dihedral_angle_1_deg 5.496 r_mcangle_it 4.785 r_mcangle_other 4.785 r_scangle_other 4.536 r_mcbond_it 2.916
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.086 r_dihedral_angle_4_deg 15.51 r_dihedral_angle_3_deg 14.914 r_long_range_B_other 7.14 r_long_range_B_refined 7.138 r_dihedral_angle_1_deg 5.496 r_mcangle_it 4.785 r_mcangle_other 4.785 r_scangle_other 4.536 r_mcbond_it 2.916 r_mcbond_other 2.914 r_scbond_it 2.625 r_scbond_other 2.624 r_angle_refined_deg 1.204 r_angle_other_deg 1.081 r_chiral_restr 0.039 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 6262 Nucleic Acid Atoms Solvent Atoms 103 Heterogen Atoms 65
Software Software Software Name Purpose REFMAC refinement Coot model building Aimless data scaling MOLREP phasing