5UVD

Crystal structure of an antigenic nucleotidyltransferase-like protein from Paracoccidioides brasiliensis


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293.150.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0
2VAPOR DIFFUSION, HANGING DROP293.150.25 M MgCl2, 25% PEG 4000, 0.1 M Tris-HCl pH 7.0 - 8,0 Crystal was incubated in a cryo-soaking solution containing 100 mM NaI and 10% (v/v) ethylene glycol
Crystal Properties
Matthews coefficientSolvent content
2.141.5
2.141.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.649α = 90
b = 51.105β = 90
c = 121.19γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2Mcollimating mirror and toroidal bendable mirror2013-05-24MSINGLE WAVELENGTH
22x-ray100CCDMAR CCD 165 mmcollimating mirror and toroidal bendable mirror2014-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.4587LNLSW01B-MX2
2SYNCHROTRONLNLS BEAMLINE W01B-MX21.4587LNLSW01B-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
21.6831.7786.10.03918.51.939751-322.5
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)
21.681.7168.90.1723.71.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT1.8647.091699989597.850.162160.159090.22168RANDOM17.673
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]
-0.932.25-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.061
r_dihedral_angle_4_deg20.954
r_dihedral_angle_3_deg13.741
r_long_range_B_refined5.573
r_dihedral_angle_1_deg5.236
r_long_range_B_other5.236
r_scangle_other3.578
r_scbond_it2.308
r_scbond_other2.308
r_mcangle_other1.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.061
r_dihedral_angle_4_deg20.954
r_dihedral_angle_3_deg13.741
r_long_range_B_refined5.573
r_dihedral_angle_1_deg5.236
r_long_range_B_other5.236
r_scangle_other3.578
r_scbond_it2.308
r_scbond_other2.308
r_mcangle_other1.909
r_mcangle_it1.908
r_angle_refined_deg1.878
r_mcbond_it1.338
r_mcbond_other1.325
r_angle_other_deg1.075
r_chiral_restr0.111
r_bond_refined_d0.02
r_gen_planes_refined0.009
r_bond_other_d0.006
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 Atoms1718
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms3

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
XDSdata processing
DENZOdata processing
XDSdata scaling
HKL-2000data scaling
AutoSolphasing