5OO9

Streptomyces PAC13 (Y55F) with uridine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.1 M MES pH 6.5, 0.2 M NH4SO4, 30 % w/v 5K PEGMME
Crystal Properties
Matthews coefficientSolvent content
2.5151.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.604α = 90
b = 66.604β = 90
c = 54.257γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E SUPERBRIGHT1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.5957.6892.80.99942.23.817643
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.591.6867.50.828.41.8

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.5957.681678283792.010.161950.160140.20003RANDOM15.196
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]
-0.13-0.07-0.130.43
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.835
r_dihedral_angle_1_deg13.366
r_dihedral_angle_4_deg12.274
r_dihedral_angle_3_deg11.809
r_long_range_B_refined5.6
r_long_range_B_other5.598
r_scangle_other2.197
r_scbond_it1.325
r_scbond_other1.325
r_angle_refined_deg1.223
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.835
r_dihedral_angle_1_deg13.366
r_dihedral_angle_4_deg12.274
r_dihedral_angle_3_deg11.809
r_long_range_B_refined5.6
r_long_range_B_other5.598
r_scangle_other2.197
r_scbond_it1.325
r_scbond_other1.325
r_angle_refined_deg1.223
r_mcangle_it1.218
r_mcangle_other1.217
r_mcbond_other0.713
r_mcbond_it0.712
r_angle_other_deg0.706
r_chiral_restr0.084
r_gen_planes_refined0.008
r_bond_refined_d0.005
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 Atoms975
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling