3CBR

Crystal structure of human Transthyretin (TTR) at pH3.5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BMZPDB ENTRY 1BMZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP3.52895-7 mg/ml protein, 0.1 M sodium acetate, 20 % PEG 3350, 0.3-0.5 M ammonium sulfate equilibrated against 2.0M ammonium sulfate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0941.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.124α = 90
b = 85.494β = 90
c = 62.419γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42003-07-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.6335.5898.20.05419.362934829348
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.631.6588.60.692.69

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1BMZ1.735.582441224412131498.490.224720.224720.222840.26048RANDOM23.883
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]
-0.1-0.190.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.846
r_dihedral_angle_3_deg13.811
r_dihedral_angle_4_deg9.807
r_dihedral_angle_1_deg5.725
r_scangle_it2.914
r_scbond_it1.738
r_mcangle_it1.251
r_angle_refined_deg1.081
r_mcbond_it0.749
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.846
r_dihedral_angle_3_deg13.811
r_dihedral_angle_4_deg9.807
r_dihedral_angle_1_deg5.725
r_scangle_it2.914
r_scbond_it1.738
r_mcangle_it1.251
r_angle_refined_deg1.081
r_mcbond_it0.749
r_nbtor_refined0.304
r_nbd_refined0.185
r_symmetry_hbond_refined0.181
r_symmetry_vdw_refined0.166
r_xyhbond_nbd_refined0.129
r_chiral_restr0.075
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1609
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms

Software

Software
Software NamePurpose
EPMRphasing
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling