9H7L | pdb_00009h7l

Human Transthyretin in Complex with 4-phenyl-1H-pyrazolo[3,4-b]pyridin-3-amine


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
2.1442.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.503α = 90
b = 84.336β = 90
c = 65.742γ = 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 ID290.9763ESRFID29

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
11.185099.30.0510.02513.84.9277826
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)
11.181.2196.30.6520.375

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 REPLACEMENTTHROUGHOUT1.1835.6973851392399.140.172610.171540.17510.192340.1926RANDOM16.203
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]
0.050.02-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.116
r_sphericity_free15.468
r_dihedral_angle_4_deg11.418
r_dihedral_angle_3_deg10.092
r_sphericity_bonded10.024
r_rigid_bond_restr7.33
r_dihedral_angle_1_deg6.015
r_scangle_other3.575
r_long_range_B_refined3.527
r_long_range_B_other3.526
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.116
r_sphericity_free15.468
r_dihedral_angle_4_deg11.418
r_dihedral_angle_3_deg10.092
r_sphericity_bonded10.024
r_rigid_bond_restr7.33
r_dihedral_angle_1_deg6.015
r_scangle_other3.575
r_long_range_B_refined3.527
r_long_range_B_other3.526
r_scbond_it3.083
r_scbond_other3.082
r_mcangle_it2.767
r_mcangle_other2.766
r_mcbond_it2.455
r_mcbond_other2.455
r_angle_refined_deg2.314
r_angle_other_deg0.948
r_chiral_restr0.121
r_bond_refined_d0.023
r_gen_planes_refined0.014
r_bond_other_d0.003
r_gen_planes_other0.001
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 Atoms1644
Nucleic Acid Atoms
Solvent Atoms98
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing