5CLY

X-ray structure of TTR mutant - S52P at 1.23A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4PVL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.52982.5M di-sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.3247.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.017α = 90
b = 85.929β = 90
c = 63.964γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2014-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.97242ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)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
11.2363.96497.50.0420.0490.02413.53.86766267662
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.231.394.10.7250.7250.4171.13.89390

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4PVL1.2335.764225340997.180.15850.1570.1857RANDOM25.514
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]
0.13-0.01-0.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.172
r_sphericity_bonded24.356
r_rigid_bond_restr15.98
r_dihedral_angle_4_deg14.817
r_dihedral_angle_3_deg13.703
r_dihedral_angle_1_deg6.403
r_mcangle_it4.871
r_mcbond_it4.763
r_mcbond_other4.234
r_angle_other_deg3.536
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.172
r_sphericity_bonded24.356
r_rigid_bond_restr15.98
r_dihedral_angle_4_deg14.817
r_dihedral_angle_3_deg13.703
r_dihedral_angle_1_deg6.403
r_mcangle_it4.871
r_mcbond_it4.763
r_mcbond_other4.234
r_angle_other_deg3.536
r_angle_refined_deg2.062
r_chiral_restr0.134
r_bond_refined_d0.023
r_gen_planes_other0.02
r_gen_planes_refined0.012
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1794
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms12

Software

Software
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling
Cootmodel building
MOLREPphasing