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Crystal structure of human transthyretin variant A25T - #1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CFM PDB entry 3CFM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 293 1 uL 5 mg/mL TTR + 1 uL well solution composed by 0.1 M Hepes sodium pH 7.5, 28 % PEG 400, 0.2 calcium chloride dihydrate (Hampton's Crystal Screen I#14), VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.08 α = 90 b = 87.83 β = 90 c = 66.55 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 MARMOSAIC 225 mm CCD 2008-03-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON LNLS BEAMLINE W01B-MX2 1.459 LNLS W01B-MX2
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 1.65 66.55 99.9 0.057 7.6 32521 2 2 20.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.65 1.69 100 0.33 0.33 5.1 7.4 4654
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 PDB entry 3CFM 1.65 23.03 32483 1647 99.81 0.204 0.203 0.2071 0.227 0.23 RANDOM 25.662
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] -0.75 0.1 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.126 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_4_deg 12.756 r_dihedral_angle_1_deg 5.349 r_scangle_it 2.438 r_scbond_it 1.463 r_mcangle_it 1.123 r_angle_refined_deg 1.113 r_mcbond_it 0.589 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.126 r_dihedral_angle_3_deg 13.306 r_dihedral_angle_4_deg 12.756 r_dihedral_angle_1_deg 5.349 r_scangle_it 2.438 r_scbond_it 1.463 r_mcangle_it 1.123 r_angle_refined_deg 1.113 r_mcbond_it 0.589 r_chiral_restr 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1789 Nucleic Acid Atoms Solvent Atoms 263 Heterogen Atoms 20
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction MAR345dtb data collection