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Crystal structure of V30M mutated transthyretin in complex with gamma-mangostin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PWE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 16% PEG400, 0.1 M NaOAc, 0.2 M CaCl2
Crystal Properties Matthews coefficient Solvent content 1.69 27.22
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.415 α = 90 b = 85.806 β = 90 c = 64.073 γ = 90
Symmetry Space Group P 21 21 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 270 2013-11-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.49 50 97.7 0.045 49.6 6 38590
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.49 1.53 95.6 0.274 4.3 3.8
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 4PWE 1.49 33.15 36655 1930 97.32 0.18584 0.18407 0.1858 0.21888 0.2207 RANDOM 20.814
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] 0.02 -0.48 0.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.833 r_dihedral_angle_4_deg 14.237 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 6.498 r_angle_refined_deg 1.829 r_chiral_restr 0.118 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.833 r_dihedral_angle_4_deg 14.237 r_dihedral_angle_3_deg 12.933 r_dihedral_angle_1_deg 6.498 r_angle_refined_deg 1.829 r_chiral_restr 0.118 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1785 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 62
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHENIX phasing