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Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2DW4 PDB ENTRY 2DW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 278 3-10% PEG 2000 Monomethyl ether, 0.1M Hepes pH 7.5, 0.2M magnesium chloride, 0.1M cacodylate, 5mM Tranylcypromine-derivative, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal Properties Matthews coefficient Solvent content 3.61 65.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.84 α = 90 b = 183.84 β = 90 c = 109.15 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 315 2008-04-15 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.000000 SPring-8 BL41XU 2 SYNCHROTRON SPRING-8 BEAMLINE BL26B2 1.000000 SPring-8 BL26B2
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 1,2 3.2 50 99 0.226 9.77 8.7 18396
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3.21 3.34 98.2 0.612 0.612 2.11 4.4 2820
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) 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 2DW4 3.2 47.73 2.1 18396 893 99.8 0.231 0.231 0.2275 0.272 0.2159 RANDOM 58.9
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] 9.78 9.78 -19.57
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_mcangle_it 1.07 c_angle_deg 0.9 c_scangle_it 0.86 c_improper_angle_d 0.7 c_mcbond_it 0.57 c_scbond_it 0.47 c_bond_d 0.003 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 20.9 c_mcangle_it 1.07 c_angle_deg 0.9 c_scangle_it 0.86 c_improper_angle_d 0.7 c_mcbond_it 0.57 c_scbond_it 0.47 c_bond_d 0.003 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5049 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 68
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing CNS refinement HKL-2000 data reduction SCALEPACK data scaling