3KGT

V30M mutant human transthyretin (TTR) complexed with genistein (V30M:GEN) pH 7.5


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52930.2 M CaCl2, 0.1 M HEPES pH 7.5, 28% PEG 400, vapor diffusion, hanging drop, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.27α = 90
b = 85.07β = 90
c = 64.18γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2009-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.4586LNLSD03B-MX1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.953097.70.0734.317463
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.952.020.0734.3

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTION1.9528.3617392884970.1990.1960.24124.31
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.417
r_dihedral_angle_3_deg14.494
r_dihedral_angle_4_deg10.361
r_dihedral_angle_1_deg5.584
r_scangle_it2.598
r_scbond_it1.606
r_mcangle_it1.195
r_angle_refined_deg1.163
r_mcbond_it0.636
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.417
r_dihedral_angle_3_deg14.494
r_dihedral_angle_4_deg10.361
r_dihedral_angle_1_deg5.584
r_scangle_it2.598
r_scbond_it1.606
r_mcangle_it1.195
r_angle_refined_deg1.163
r_mcbond_it0.636
r_nbtor_refined0.307
r_symmetry_vdw_refined0.256
r_symmetry_hbond_refined0.233
r_nbd_refined0.207
r_xyhbond_nbd_refined0.131
r_chiral_restr0.076
r_bond_refined_d0.009
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1769
Nucleic Acid Atoms
Solvent Atoms155
Heterogen Atoms40

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction