5JY5

Crystal structure of Thioredoxin 1 from Cryptococcus neoformans at 1.8 Angstroms resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.72941.6 M ammonium sulfate, 0.02 M tris hydrochloride
Crystal Properties
Matthews coefficientSolvent content
3.3463.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.706α = 90
b = 110.706β = 90
c = 91.763γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.2398LNLSW01B-MX2

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
11.8251000.09252.937.131224
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)
11.81.861000.5816.234.7

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 REPLACEMENTTHROUGHOUT2J231.895.8729599154299.730.158260.156340.19549RANDOM37.274
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]
-0.9-0.45-0.92.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.487
r_dihedral_angle_3_deg14.354
r_long_range_B_refined8.52
r_long_range_B_other8.275
r_dihedral_angle_1_deg5.607
r_scangle_other4.659
r_scbond_it3.137
r_scbond_other3.081
r_mcangle_it2.324
r_mcangle_other2.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.487
r_dihedral_angle_3_deg14.354
r_long_range_B_refined8.52
r_long_range_B_other8.275
r_dihedral_angle_1_deg5.607
r_scangle_other4.659
r_scbond_it3.137
r_scbond_other3.081
r_mcangle_it2.324
r_mcangle_other2.323
r_angle_refined_deg2.189
r_mcbond_it1.708
r_mcbond_other1.675
r_angle_other_deg1.139
r_chiral_restr0.145
r_bond_refined_d0.023
r_gen_planes_refined0.012
r_bond_other_d0.003
r_gen_planes_other0.002
r_dihedral_angle_4_deg
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 Atoms1632
Nucleic Acid Atoms
Solvent Atoms347
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing