5YW2

Crystal structure of Adenine phosphoribosyltransferase from Francisella tularensis.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.2M Magnesium chloride, 0.1M HEPES:NaOH pH 7.5, 25% PEG 3350, cryo 0.5M Lithium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.4549.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.168α = 90
b = 82.147β = 90
c = 170.119γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2015-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.953ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
12.2835.3699.30.0820.0840.0299.3935141
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.282.321000.9710.3320.939.2

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 REPLACEMENTTHROUGHOUT4MB62.2835.3633294172999.060.204810.201950.25875RANDOM49.396
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]
-0.083.13-3.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.511
r_dihedral_angle_4_deg18.464
r_dihedral_angle_3_deg17.293
r_dihedral_angle_1_deg7.859
r_long_range_B_refined6.058
r_long_range_B_other6.029
r_scangle_other4.215
r_mcangle_it3.765
r_mcangle_other3.765
r_scbond_it2.554
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.511
r_dihedral_angle_4_deg18.464
r_dihedral_angle_3_deg17.293
r_dihedral_angle_1_deg7.859
r_long_range_B_refined6.058
r_long_range_B_other6.029
r_scangle_other4.215
r_mcangle_it3.765
r_mcangle_other3.765
r_scbond_it2.554
r_scbond_other2.55
r_mcbond_it2.296
r_mcbond_other2.293
r_angle_refined_deg2.068
r_angle_other_deg1.081
r_chiral_restr0.115
r_bond_refined_d0.021
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms5358
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing