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Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5IT3 PDB ENTRY 5IT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.1 M Bis-Tris, pH 6.5, 0.1 M potassium chloride, 1.5 M ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 1.7 27.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.957 α = 90 b = 57.514 β = 90 c = 97.019 γ = 90
Symmetry Space Group P 21 21 21
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 MARMOSAIC 300 mm CCD 2018-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-G 0.97857 APS 21-ID-G
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 1.16 35.18 96.8 0.072 50.7 11.4 94426
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.16 1.19 86.4 0.507 3.5 8.7
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 PDB ENTRY 5IT3 1.16 35.18 92362 2000 96.8 0.133 0.133 0.1326 0.169 0.1687 RANDOM 14.21
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] -0.01 -0.14 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.086 r_sphericity_free 22.147 r_dihedral_angle_4_deg 19.467 r_dihedral_angle_3_deg 12.753 r_sphericity_bonded 12.715 r_dihedral_angle_1_deg 5.803 r_long_range_B_refined 4.036 r_scangle_other 3.988 r_long_range_B_other 3.873 r_rigid_bond_restr 3.469
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.086 r_sphericity_free 22.147 r_dihedral_angle_4_deg 19.467 r_dihedral_angle_3_deg 12.753 r_sphericity_bonded 12.715 r_dihedral_angle_1_deg 5.803 r_long_range_B_refined 4.036 r_scangle_other 3.988 r_long_range_B_other 3.873 r_rigid_bond_restr 3.469 r_scbond_it 3.335 r_scbond_other 3.233 r_mcangle_it 2.756 r_mcangle_other 2.755 r_mcbond_it 2.215 r_mcbond_other 2.215 r_angle_refined_deg 1.907 r_angle_other_deg 1.192 r_chiral_restr 0.102 r_bond_refined_d 0.015 r_gen_planes_refined 0.01 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2885 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing