9H7K | pdb_00009h7k

Human Transthyretin in Complex with 8-(3,5-dimethyl-1H-pyrazol-4-yl)quinoline


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
1.9737.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.107α = 90
b = 63.069β = 90
c = 83.837γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAPEX II CCD2012-10-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEBRUKER D8 QUEST1.542

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
11.663.0798.60.0430.02217.784.0729346
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)
11.61.6380.1760.145

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 REPLACEMENTTHROUGHOUT1.650.427814149298.630.179250.176310.18950.235520.2444RANDOM15.248
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]
0.59-0.37-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_sphericity_free21.215
r_dihedral_angle_4_deg16.734
r_sphericity_bonded14.026
r_dihedral_angle_3_deg13.366
r_dihedral_angle_1_deg7.408
r_rigid_bond_restr4.935
r_angle_refined_deg1.962
r_angle_other_deg0.859
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.108
r_sphericity_free21.215
r_dihedral_angle_4_deg16.734
r_sphericity_bonded14.026
r_dihedral_angle_3_deg13.366
r_dihedral_angle_1_deg7.408
r_rigid_bond_restr4.935
r_angle_refined_deg1.962
r_angle_other_deg0.859
r_chiral_restr0.107
r_bond_refined_d0.02
r_gen_planes_refined0.012
r_gen_planes_other0.003
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1614
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
PROTEUM PLUSdata reduction
PROTEUM PLUSdata scaling
PHASERphasing