5OOA

Streptomyces PAC13 (Y89F) with uridine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2 M ammonium fluoride, 20 % w/v PEG-3350
Crystal Properties
Matthews coefficientSolvent content
2.5451.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.792α = 90
b = 66.792β = 90
c = 54.56γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN A2002016-02-17MSINGLE 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
11.657.8495.30.99837.33.317880
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)
11.61.7176.80.8587.61.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1.657.841694784794.610.159320.158090.18537RANDOM15.146
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]
-0.18-0.09-0.180.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.919
r_dihedral_angle_4_deg13.991
r_dihedral_angle_1_deg13.904
r_dihedral_angle_3_deg11.533
r_long_range_B_refined5.871
r_long_range_B_other5.868
r_scangle_other2.783
r_scbond_it1.712
r_scbond_other1.712
r_mcangle_it1.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.919
r_dihedral_angle_4_deg13.991
r_dihedral_angle_1_deg13.904
r_dihedral_angle_3_deg11.533
r_long_range_B_refined5.871
r_long_range_B_other5.868
r_scangle_other2.783
r_scbond_it1.712
r_scbond_other1.712
r_mcangle_it1.47
r_mcangle_other1.469
r_angle_refined_deg1.255
r_mcbond_it0.867
r_mcbond_other0.863
r_angle_other_deg0.737
r_chiral_restr0.086
r_gen_planes_refined0.008
r_bond_refined_d0.007
r_bond_other_d0.006
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 Atoms197
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling