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Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
Crystal Properties Matthews coefficient Solvent content 6 79.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.949 α = 90 b = 178.646 β = 90 c = 234.93 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 CUSTOM 2006-12-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM APS 19-BM
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.69 48.57 99.9 0.05 36.6 9.9 69440 -3 81.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.69 2.71 98.5 0.68 1.8 8.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 OTHER THROUGHOUT 2.72 49 66383 1502 99.9 0.242 0.241 0.2308 0.272 0.2484 RANDOM 64.3
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] 6.3 -3.64 -2.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.073 r_dihedral_angle_3_deg 16.083 r_dihedral_angle_4_deg 14.126 r_scangle_it 1.668 r_dihedral_angle_1_deg 1.593 r_angle_refined_deg 1.205 r_scbond_it 0.923 r_mcangle_it 0.875 r_mcbond_it 0.508 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.073 r_dihedral_angle_3_deg 16.083 r_dihedral_angle_4_deg 14.126 r_scangle_it 1.668 r_dihedral_angle_1_deg 1.593 r_angle_refined_deg 1.205 r_scbond_it 0.923 r_mcangle_it 0.875 r_mcbond_it 0.508 r_nbtor_refined 0.302 r_symmetry_hbond_refined 0.198 r_nbd_refined 0.192 r_symmetry_vdw_refined 0.161 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.081 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_other r_long_range_B_refined 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 6337 Nucleic Acid Atoms Solvent Atoms 51 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling