4POB

Crystal structure of a thioredoxin Rv1471 ortholog from Mycobacterium abscessus


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2L4Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.9289SSGCID-MyabA.01255.a at 15.42 mg/mL against MCSG screen condition B4, 0.2 M sodium thiocyanate pH 6.9, 25% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 252343d4, unique puck ID ekd3-10, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.8934.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 37.5α = 90
b = 47.49β = 90
c = 108.75γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2014-02-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.75098.50.05120.224.821770-325.696
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)
11.71.7499.90.5233.03

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 REPLACEMENTTHROUGHOUT2L4Q1.730.872089399994.520.16690.16540.1977RANDOM21.873
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]
0.10.01-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.282
r_dihedral_angle_4_deg15.98
r_dihedral_angle_3_deg11.974
r_dihedral_angle_1_deg5.706
r_mcangle_it1.548
r_angle_refined_deg1.517
r_mcbond_it0.981
r_mcbond_other0.981
r_angle_other_deg0.835
r_chiral_restr0.093
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.282
r_dihedral_angle_4_deg15.98
r_dihedral_angle_3_deg11.974
r_dihedral_angle_1_deg5.706
r_mcangle_it1.548
r_angle_refined_deg1.517
r_mcbond_it0.981
r_mcbond_other0.981
r_angle_other_deg0.835
r_chiral_restr0.093
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1574
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms5

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
BALBESphasing