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Human TTR altered by a rhenium tris-carbonyl Pyta-C8 derivative
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4PME
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 293 protein: 10 mg/ml Dialysed in 100 milli-M NaCl, 50 milli-M sodium acetate, pH 5.5
precipitant: 21% polyethylene glycol 4,000 (PEG4K), 0.14 M imidazole malate, pH 6.0
cryosoak: 40% SM2 (12.5 % ethylene glycol, 12.5 % glycerol, 12.5 %
1,2-propanediol, 25 % DMSO and 37.5% 1,4-dioxane) 50% PEG 8K and 0.2 milli-M of rhenium tris-carbonyl Pyta-C8 derivative.
Crystal Properties Matthews coefficient Solvent content 2.29 46.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.82 α = 90 b = 83.1 β = 90 c = 65.34 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 EIGER X 16M mirrors 2016-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 1.175919 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) CC (Half) 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 1.69 50 99.1 0.033 0.028 1 22.92 3.45 49863 -3
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 1.69 1.74 92.4 0.631 2.22 2.88
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4PME 1.69 41.55 25309 1332 99.59 0.17391 0.17134 0.22199 0.2365 RANDOM 30.101
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] -1.07 -0.14 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_4_deg 20.511 r_dihedral_angle_3_deg 15.686 r_long_range_B_refined 10.625 r_long_range_B_other 10.623 r_scangle_other 7.589 r_dihedral_angle_1_deg 6.537 r_scbond_it 4.957 r_scbond_other 4.955 r_mcangle_it 4.578
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_4_deg 20.511 r_dihedral_angle_3_deg 15.686 r_long_range_B_refined 10.625 r_long_range_B_other 10.623 r_scangle_other 7.589 r_dihedral_angle_1_deg 6.537 r_scbond_it 4.957 r_scbond_other 4.955 r_mcangle_it 4.578 r_mcangle_other 4.577 r_mcbond_it 3.202 r_mcbond_other 3.169 r_angle_refined_deg 2.027 r_angle_other_deg 1.057 r_chiral_restr 0.15 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1792 Nucleic Acid Atoms Solvent Atoms 167 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing