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Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4I4T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 PEG 4000, Glycerol, Magnesium chloride, Calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.97 58.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.357 α = 90 b = 157.252 β = 90 c = 179.631 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 ADSC QUANTUM 315r 2015-01-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9795 SSRF BL17U
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 99.9 11.6 7.4 131984
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4I4T 2.3 47.636 1.34 131273 6500 99.81 0.1822 0.1813 0.1831 0.1999 0.2016
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 21.456 f_angle_d 1.035 f_chiral_restr 0.063 f_bond_d 0.008 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17043 Nucleic Acid Atoms Solvent Atoms 557 Heterogen Atoms 309
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection HKL-2000 data scaling PHASER phasing