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Crystal structure of dioscorin complexed with ascorbate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 278 BICINE, PEG400, ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.43 49.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.505 α = 90 b = 157.103 β = 90 c = 83.485 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2011-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.11 20 99 0.045 51.6 6.5 31531
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 THROUGHOUT 2.11 20 29858 1598 98.44 0.20476 0.20132 0.2077 0.26604 0.2593 RANDOM 42.186
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] 0.12 -1.71 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_4_deg 16.629 r_long_range_B_refined 8.576 r_long_range_B_other 8.575 r_dihedral_angle_1_deg 7.288 r_scangle_other 6.365 r_mcangle_it 4.81 r_mcangle_other 4.81 r_scbond_it 4.354
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.094 r_dihedral_angle_3_deg 18.446 r_dihedral_angle_4_deg 16.629 r_long_range_B_refined 8.576 r_long_range_B_other 8.575 r_dihedral_angle_1_deg 7.288 r_scangle_other 6.365 r_mcangle_it 4.81 r_mcangle_other 4.81 r_scbond_it 4.354 r_scbond_other 4.339 r_mcbond_it 3.566 r_mcbond_other 3.564 r_angle_refined_deg 1.941 r_angle_other_deg 0.893 r_chiral_restr 0.12 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3849 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement