9H7G | pdb_00009h7g

Human Transthyretin in Complex with 1H-indole-3-carbonitrile


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
2.0841

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.12α = 90
b = 42.18β = 90
c = 64γ = 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
11.4951.1599.90.0540.01626.11338414
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)
11.491.530.7110.219

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 REPLACEMENTTHROUGHOUT1.4951.1536454191899.860.162510.159990.15860.209940.2119RANDOM19.842
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]
-0.270.41-0.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.919
r_sphericity_free16.269
r_sphericity_bonded12.056
r_dihedral_angle_3_deg12.053
r_dihedral_angle_4_deg11.166
r_rigid_bond_restr6.718
r_dihedral_angle_1_deg5.824
r_scangle_other5.03
r_long_range_B_refined4.998
r_long_range_B_other4.997
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.919
r_sphericity_free16.269
r_sphericity_bonded12.056
r_dihedral_angle_3_deg12.053
r_dihedral_angle_4_deg11.166
r_rigid_bond_restr6.718
r_dihedral_angle_1_deg5.824
r_scangle_other5.03
r_long_range_B_refined4.998
r_long_range_B_other4.997
r_scbond_it4.777
r_scbond_other4.775
r_mcangle_it3.997
r_mcangle_other3.997
r_mcbond_it3.254
r_mcbond_other3.252
r_angle_refined_deg1.965
r_angle_other_deg0.827
r_chiral_restr0.123
r_bond_refined_d0.02
r_gen_planes_refined0.011
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 Atoms1659
Nucleic Acid Atoms
Solvent Atoms50
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing