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Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z5U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1 M imidazole/HCl (pH 7.0), 14% PEG 3350, 10% 2-methyl-2,4-pentanediol
Crystal Properties Matthews coefficient Solvent content 3.61 65.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 184.55 α = 90 b = 184.55 β = 90 c = 108.571 γ = 120
Symmetry Space Group P 61 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 ADSC QUANTUM 315r 2015-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.25 159.82 99.7 0.08 0.079 0.025 9.2 13.4 51851
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.29 99.1 0.525 0.654 11.6
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 2Z5U 2.25 50 49246 2576 99.68 0.1957 0.1935 0.1938 0.2382 0.2381 RANDOM 60.134
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] 0.91 0.46 0.91 -2.96
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.198 r_dihedral_angle_4_deg 18.196 r_dihedral_angle_3_deg 15.619 r_dihedral_angle_1_deg 6.512 r_angle_refined_deg 1.129 r_chiral_restr 0.072 r_gen_planes_refined 0.009 r_bond_refined_d 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5022 Nucleic Acid Atoms Solvent Atoms 208 Heterogen Atoms 73
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction