9H7O | pdb_00009h7o

Human Transthyretin in Complex with 5-(quinolin-8-yl)pyrimidin-2-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
2.0941.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 42.074α = 90
b = 85.045β = 90
c = 64.267γ = 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
11.245096.70.0450.02314.074.663682
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)
11.241.2720.5920.3271.83

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 REPLACEMENTTHROUGHOUT1.2435.4660444320896.250.161120.159440.1630.192640.1923RANDOM17.365
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]
0.06-0.10.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.399
r_sphericity_free17.747
r_dihedral_angle_3_deg10.475
r_sphericity_bonded10.203
r_dihedral_angle_4_deg8.956
r_rigid_bond_restr6.985
r_dihedral_angle_1_deg5.787
r_long_range_B_refined4.199
r_long_range_B_other4.198
r_scangle_other3.691
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.399
r_sphericity_free17.747
r_dihedral_angle_3_deg10.475
r_sphericity_bonded10.203
r_dihedral_angle_4_deg8.956
r_rigid_bond_restr6.985
r_dihedral_angle_1_deg5.787
r_long_range_B_refined4.199
r_long_range_B_other4.198
r_scangle_other3.691
r_mcangle_it3.666
r_mcangle_other3.665
r_scbond_it3.3
r_scbond_other3.298
r_mcbond_it2.815
r_mcbond_other2.814
r_angle_refined_deg1.981
r_angle_other_deg0.902
r_chiral_restr0.137
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_gen_planes_other0.002
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1687
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing