3RD5

Crystal structure of a putative uncharacterized protein from Mycobacterium Paratuberculosis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5290EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K.
2VAPOR DIFFUSION, SITTING DROP7.5290EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, FOR PHASING THIS CRYSTAL WAS TRANFERRED IN 100MM HEPES PH 7.5, 15% PEG 6000, 10% ETHYLENE GLYCOL, 400MM SODIUM IODIDE, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.92α = 90
b = 78.1β = 90
c = 86.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2011-03-04MSINGLE WAVELENGTH
22x-ray100CCDRIGAKU SATURN 944+2011-03-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.978560APS21-ID-G
2ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,21.55098.90.0490.04922.617.67010970109-322.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,21.51.541000.3890.3894.45.45161

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUTSTRUCTURE SOLVED VIA IODIDE PHASING AT CUKALPHA, DATA SET 2 WAS USED FOR THIS1.549.927010969906352698.70.1340.1340.1330.15RANDOM14.71
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]
-0.190.62-0.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.377
r_dihedral_angle_4_deg17.028
r_dihedral_angle_3_deg11.658
r_dihedral_angle_1_deg5.525
r_scangle_it4.028
r_scbond_it2.491
r_mcangle_it1.562
r_angle_refined_deg1.539
r_angle_other_deg1.019
r_mcbond_it0.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.377
r_dihedral_angle_4_deg17.028
r_dihedral_angle_3_deg11.658
r_dihedral_angle_1_deg5.525
r_scangle_it4.028
r_scbond_it2.491
r_mcangle_it1.562
r_angle_refined_deg1.539
r_angle_other_deg1.019
r_mcbond_it0.924
r_mcbond_other0.259
r_chiral_restr0.1
r_bond_refined_d0.015
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2031
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms19

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling