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Human Transthyretin in Complex with 5-methyl-4-phenyl-1H-pyrazol-3-amine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294.15 100 mM HEPES, 200 mM CaCl2, 28% v/v PEG400, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.04 39.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.48 α = 90 b = 42.02 β = 90 c = 63.49 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 PIXEL DECTRIS PILATUS 6M 2013-07-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.3 42.02 100 0.048 0.017 23.4 10.5 56419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.33 0.72 0.247
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 MOLECULAR REPLACEMENT THROUGHOUT 1.3 31.75 53512 2855 99.93 0.22705 0.22528 0.2315 0.26024 0.2645 RANDOM 17.172
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] -0.43 0.75 -0.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.187 r_sphericity_free 19.036 r_sphericity_bonded 15.06 r_dihedral_angle_3_deg 11.313 r_rigid_bond_restr 8.973 r_dihedral_angle_1_deg 6.618 r_long_range_B_refined 3.933 r_long_range_B_other 3.931 r_scangle_other 3.777 r_dihedral_angle_4_deg 3.604
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.187 r_sphericity_free 19.036 r_sphericity_bonded 15.06 r_dihedral_angle_3_deg 11.313 r_rigid_bond_restr 8.973 r_dihedral_angle_1_deg 6.618 r_long_range_B_refined 3.933 r_long_range_B_other 3.931 r_scangle_other 3.777 r_dihedral_angle_4_deg 3.604 r_mcangle_it 3.406 r_mcangle_other 3.405 r_scbond_it 3.366 r_scbond_other 3.364 r_mcbond_other 3.082 r_mcbond_it 3.08 r_angle_refined_deg 3.028 r_angle_other_deg 1.141 r_chiral_restr 0.183 r_bond_refined_d 0.031 r_gen_planes_refined 0.017 r_bond_other_d 0.002 r_gen_planes_other 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1541 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing