9H7D | pdb_00009h7d

Human Transthyretin in Complex with 2-(phenylamino)benzoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DVQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5294.15100 mM HEPES, 200 mM CaCl2, 28% v/v PEG400, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
1.9637.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.149α = 90
b = 84.076β = 90
c = 62.3γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2013-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.2339.9697.50.0610.0311.044.861779
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.26295.070.3420.167

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.2334.3458660311297.170.163430.162150.16620.187810.1907RANDOM17.536
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]
0.09-0.04-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.855
r_dihedral_angle_4_deg22.18
r_sphericity_free14.512
r_dihedral_angle_3_deg13.284
r_sphericity_bonded11.441
r_rigid_bond_restr7.328
r_dihedral_angle_1_deg6.964
r_long_range_B_refined4.607
r_long_range_B_other4.606
r_scangle_other4.437
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.855
r_dihedral_angle_4_deg22.18
r_sphericity_free14.512
r_dihedral_angle_3_deg13.284
r_sphericity_bonded11.441
r_rigid_bond_restr7.328
r_dihedral_angle_1_deg6.964
r_long_range_B_refined4.607
r_long_range_B_other4.606
r_scangle_other4.437
r_scbond_it4.091
r_scbond_other4.089
r_mcangle_other3.482
r_mcangle_it3.481
r_mcbond_it2.934
r_mcbond_other2.934
r_angle_refined_deg2.316
r_angle_other_deg1.092
r_chiral_restr0.151
r_bond_refined_d0.025
r_gen_planes_refined0.015
r_gen_planes_other0.014
r_bond_other_d0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1654
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing