4RA3

Crystal structure of dimeric S33C beta-2 microglobulin mutant in complex with Thioflavin (ThT) at 2.8 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3S6CPDB ENTRY 3S6C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829325% v/v PEG4000, 0.1 M sodium chloride, 5 mM thioflavin, 0.1 M HEPES sodium, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.4564.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.038α = 90
b = 80.038β = 90
c = 177.7γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS 6M2014-01-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.97088PETRA III, EMBL c/o DESYP13 (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
12.8177.71000.05921.49.61694016940
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)
12.82.951001.139210

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUTPDB ENTRY 3S6C2.869.31169401603686299.910.172520.170750.20649RANDOM113.054
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]
26.3426.34-52.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.454
r_dihedral_angle_4_deg28.387
r_dihedral_angle_3_deg21.408
r_long_range_B_refined13.135
r_long_range_B_other13.133
r_scangle_other10.519
r_dihedral_angle_1_deg9.926
r_mcangle_it9.81
r_mcangle_other9.734
r_scbond_it7.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.454
r_dihedral_angle_4_deg28.387
r_dihedral_angle_3_deg21.408
r_long_range_B_refined13.135
r_long_range_B_other13.133
r_scangle_other10.519
r_dihedral_angle_1_deg9.926
r_mcangle_it9.81
r_mcangle_other9.734
r_scbond_it7.33
r_scbond_other7.204
r_mcbond_it6.823
r_mcbond_other6.819
r_angle_other_deg1.548
r_angle_refined_deg1.453
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.007
r_gen_planes_other0.002
r_bond_other_d0.001
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3307
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms100

Software

Software
Software NamePurpose
MxCuBEdata collection
BALBESphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling