3DJT

Crystal structure of transthyretin variant V30M at acidic pH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1F41 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.629532% PEG 2000, 0.1M NaAc, 0.2M Am2SO4 , pH 4.6, VAPOR DIFFUSION, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.1943.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.782α = 90
b = 86.064β = 90
c = 64.231γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152006-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9859ESRFID14-4

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
12.286.0797.60.094123.31249112491
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)
12.22.3294.90.3265.531716

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1F412.351.51124911088052697.820.21510.213130.25338RANDOM31.92
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]
0.94-0.85-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg24.739
r_dihedral_angle_3_deg20.445
r_scangle_it7.112
r_dihedral_angle_1_deg6.031
r_scbond_it5.4
r_mcangle_it5.277
r_mcbond_it3.802
r_angle_refined_deg1.792
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.866
r_dihedral_angle_4_deg24.739
r_dihedral_angle_3_deg20.445
r_scangle_it7.112
r_dihedral_angle_1_deg6.031
r_scbond_it5.4
r_mcangle_it5.277
r_mcbond_it3.802
r_angle_refined_deg1.792
r_nbtor_refined0.312
r_symmetry_vdw_refined0.231
r_nbd_refined0.223
r_xyhbond_nbd_refined0.174
r_chiral_restr0.135
r_symmetry_hbond_refined0.114
r_bond_refined_d0.025
r_gen_planes_refined0.01
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 Atoms1787
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing