5NJO

Roll out the beta-barrel: structure and mechanism of Pac13, a unique nucleoside dehydratase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5NJN 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.82930.1 M Tris pH 8.8, 20% w/v PEG8K, 0.2 M MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.5251.28

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.49α = 90
b = 66.49β = 90
c = 54.71γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9797DiamondI03

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
11.5557.581000.05923.510.92063018.63
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)
11.551.6199.90.77610.6

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 REPLACEMENTTHROUGHOUT5NJN1.5557.5819574105699.970.180990.179940.20115RANDOM21.958
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]
0.160.080.16-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.481
r_dihedral_angle_4_deg15.57
r_dihedral_angle_3_deg12.328
r_long_range_B_refined8.234
r_dihedral_angle_1_deg6.948
r_long_range_B_other6.677
r_scangle_other2.872
r_scbond_it1.765
r_scbond_other1.763
r_mcangle_it1.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg26.481
r_dihedral_angle_4_deg15.57
r_dihedral_angle_3_deg12.328
r_long_range_B_refined8.234
r_dihedral_angle_1_deg6.948
r_long_range_B_other6.677
r_scangle_other2.872
r_scbond_it1.765
r_scbond_other1.763
r_mcangle_it1.625
r_mcangle_other1.624
r_angle_refined_deg1.272
r_mcbond_it0.991
r_mcbond_other0.988
r_angle_other_deg0.709
r_chiral_restr0.08
r_bond_refined_d0.006
r_gen_planes_refined0.004
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms976
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
PHASERphasing