9H7J | pdb_00009h7j

Human Transthyretin in Complex with 5-methyl-4-phenyl-1H-pyrazol-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
2.0439.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.48α = 90
b = 42.02β = 90
c = 63.49γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97949DiamondI04

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
11.342.021000.0480.01723.410.556419
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)
11.31.330.720.247

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 REPLACEMENTTHROUGHOUT1.331.7553512285599.930.227050.225280.23150.260240.2645RANDOM17.172
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]
-0.430.75-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.187
r_sphericity_free19.036
r_sphericity_bonded15.06
r_dihedral_angle_3_deg11.313
r_rigid_bond_restr8.973
r_dihedral_angle_1_deg6.618
r_long_range_B_refined3.933
r_long_range_B_other3.931
r_scangle_other3.777
r_dihedral_angle_4_deg3.604
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.187
r_sphericity_free19.036
r_sphericity_bonded15.06
r_dihedral_angle_3_deg11.313
r_rigid_bond_restr8.973
r_dihedral_angle_1_deg6.618
r_long_range_B_refined3.933
r_long_range_B_other3.931
r_scangle_other3.777
r_dihedral_angle_4_deg3.604
r_mcangle_it3.406
r_mcangle_other3.405
r_scbond_it3.366
r_scbond_other3.364
r_mcbond_other3.082
r_mcbond_it3.08
r_angle_refined_deg3.028
r_angle_other_deg1.141
r_chiral_restr0.183
r_bond_refined_d0.031
r_gen_planes_refined0.017
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms1541
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms28

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing