3P3R

Transthyretin in complex with (3,4-dihydroxy-5-nitrophenyl)(2-fluorophenyl)methanone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2FBRPDB entry 2FBR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.5298The WT-TTR was concentrated to 4 mg/mL in 10 mM NaPi, 100 mM KCl, at pH 7.6 and co-crystallized at room temperature using the vapor-diffusion sitting drop method. Crystals were grown from 1.395 M sodium citrate, 3.5% v/v glycerol at pH 5.5. The crystals were frozen using a cryo-protectant solution of 1.395 M sodium citrate, pH 5.5, containing 10% v/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1242.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.848α = 90
b = 84.914β = 90
c = 64.35γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARMOSAIC 325 mm CCDFlat mirror (vertical focusing), single crystal Si(111) bent monochromator (ho rizontal focusing)2010-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.97945SSRLBL11-1

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
11.255099.70.02956.57.26551615.3
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)RedundancyNumber Unique Reflections (All)
11.251.291000.0290.0366.96478

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2FBR1.255065467331599.560.15580.15460.1796RANDOM21.8142
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]
-0.020.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.034
r_dihedral_angle_4_deg19.396
r_dihedral_angle_3_deg13.268
r_sphericity_free9.903
r_dihedral_angle_1_deg6.506
r_scangle_it6.31
r_sphericity_bonded5.542
r_scbond_it4.251
r_mcangle_it3.384
r_mcbond_it2.182
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.034
r_dihedral_angle_4_deg19.396
r_dihedral_angle_3_deg13.268
r_sphericity_free9.903
r_dihedral_angle_1_deg6.506
r_scangle_it6.31
r_sphericity_bonded5.542
r_scbond_it4.251
r_mcangle_it3.384
r_mcbond_it2.182
r_rigid_bond_restr2.094
r_angle_refined_deg1.953
r_angle_other_deg1.059
r_mcbond_other0.944
r_chiral_restr0.109
r_bond_refined_d0.02
r_gen_planes_refined0.01
r_bond_other_d0.007
r_gen_planes_other0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1785
Nucleic Acid Atoms
Solvent Atoms280
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing