3OZL

Crystal structure of human transthyretin variant A25T in complex with flufenamic acid.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I9APDB entry 3I9A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.1 M Hepes sodium pH 7.5, 28% PEG 400, 0.2 calcium chloride dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K, soaking for 1 h with ligand.
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.93α = 90
b = 85.607β = 90
c = 65.228γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2008-03-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4586LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.965.23398.60.0570.05717.54.6196971969724.6
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)
11.9297.60.310.312.44.62811

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 3I9A1.926.1419685100998.160.20110.19870.2474RANDOM24.2611
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]
1.07-0.85-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.694
r_dihedral_angle_4_deg18.273
r_dihedral_angle_3_deg15.72
r_dihedral_angle_1_deg5.891
r_scangle_it2.383
r_scbond_it1.64
r_angle_refined_deg1.368
r_mcangle_it1.231
r_mcbond_it0.712
r_nbtor_refined0.298
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.694
r_dihedral_angle_4_deg18.273
r_dihedral_angle_3_deg15.72
r_dihedral_angle_1_deg5.891
r_scangle_it2.383
r_scbond_it1.64
r_angle_refined_deg1.368
r_mcangle_it1.231
r_mcbond_it0.712
r_nbtor_refined0.298
r_symmetry_vdw_refined0.238
r_nbd_refined0.204
r_xyhbond_nbd_refined0.146
r_symmetry_hbond_refined0.134
r_chiral_restr0.083
r_bond_refined_d0.014
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1789
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms40

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection