X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4KX4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.6293.15Protein solution: 25mg/ml in 25mM Tris pH 8.0, 150 mM NaCl, 20 mM GSH, 10 mM DHA Reservoir condition: 0.2M Ammonium acetate, 0.1M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000. Protein and reservoir mixed in 1:1, 1:2 and 2:1 ratio, set up using MRC Swissci 3 well plates with drop size of 150 nl.
Crystal Properties
Matthews coefficientSolvent content
2.1442.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.84α = 90
b = 169.451β = 93.51
c = 49.842γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 4M2017-07-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-30.968ESRFMASSIF-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.44942.9494.70.0990.1130.0550.9978.74.2137631
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.4491.47689.20.6350.7260.3490.7594.2

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 REPLACEMENTTHROUGHOUT4KX41.4542.893131485687795.080.13940.13830.1604RANDOM11.935
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]
-0.450.170.72-0.28
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.579
r_dihedral_angle_4_deg16.072
r_dihedral_angle_3_deg11.312
r_dihedral_angle_1_deg6.557
r_angle_refined_deg1.881
r_angle_other_deg1.687
r_chiral_restr0.333
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.579
r_dihedral_angle_4_deg16.072
r_dihedral_angle_3_deg11.312
r_dihedral_angle_1_deg6.557
r_angle_refined_deg1.881
r_angle_other_deg1.687
r_chiral_restr0.333
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6813
Nucleic Acid Atoms
Solvent Atoms1314
Heterogen Atoms119

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing