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Crystal structure of Lysine-specific demethylase1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 277 0.1mM Hepes-Na, 5% MPD, 3-4.5% PEG monomethylether 2000, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal Properties Matthews coefficient Solvent content 3.68 66.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 185.742 α = 90 b = 185.742 β = 90 c = 108.725 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 298 CCD ADSC QUANTUM 315 2007-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.25 50 97.2 0.075 21.91 3.6 51737 49205 -3 31.4
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) 2.25 2.33 88.6 0.372 2.1 3.2 4607
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 FOURIER SYNTHESIS THROUGHOUT 2.25 35.36 49205 2448 97.2 0.2179 0.2179 0.2188 0.25475 0.207 RANDOM 51.7
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] 5.75 5.27 5.75 -11.5
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 3.24 c_mcangle_it 2.26 c_scbond_it 2.18 c_angle_deg 1.4 c_mcbond_it 1.35 c_improper_angle_d 0.95 c_bond_d 0.009 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.5 c_scangle_it 3.24 c_mcangle_it 2.26 c_scbond_it 2.18 c_angle_deg 1.4 c_mcbond_it 1.35 c_improper_angle_d 0.95 c_bond_d 0.009 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 5052 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 63
Software Software Software Name Purpose CNS refinement HKL-2000 data collection DENZO data reduction HKL-2000 data scaling CNS phasing