9H7H | pdb_00009h7h

Human Transthyretin in Complex with Isoquinolin-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
2.1442.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.64α = 90
b = 42.5β = 90
c = 64.93γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.92DiamondI04-1

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
11.4735.7599.80.0550.01722.712.841047
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)
11.471.510.6620.215

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 REPLACEMENTTHROUGHOUT1.4735.7538944205999.770.164410.161740.16750.215080.2198RANDOM19.272
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]
-0.080.22-0.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.436
r_dihedral_angle_4_deg21.384
r_sphericity_free17.515
r_dihedral_angle_3_deg12.846
r_sphericity_bonded12.017
r_rigid_bond_restr7.313
r_dihedral_angle_1_deg5.857
r_scangle_other4.758
r_long_range_B_refined4.677
r_long_range_B_other4.675
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.436
r_dihedral_angle_4_deg21.384
r_sphericity_free17.515
r_dihedral_angle_3_deg12.846
r_sphericity_bonded12.017
r_rigid_bond_restr7.313
r_dihedral_angle_1_deg5.857
r_scangle_other4.758
r_long_range_B_refined4.677
r_long_range_B_other4.675
r_scbond_it4.389
r_scbond_other4.387
r_mcangle_it3.977
r_mcangle_other3.975
r_mcbond_it3.461
r_mcbond_other3.365
r_angle_refined_deg1.819
r_angle_other_deg0.866
r_chiral_restr0.117
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.001
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 Atoms1682
Nucleic Acid Atoms
Solvent Atoms97
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing