5OO8

Streptomyces PAC13 (H42Q) with uridine


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2930.2 M potassium sodium tartrate, 20 % w/v PEG-335
Crystal Properties
Matthews coefficientSolvent content
2.5551.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.39α = 90
b = 66.39β = 90
c = 54.841γ = 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)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
11.7857.599.50.05119.23.613630
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)
11.781.9299.70.3763.43.4

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 REPLACEMENTTHROUGHOUT1.7857.51290067299.070.166730.16540.19407RANDOM21.196
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]
-0.24-0.12-0.240.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.308
r_dihedral_angle_3_deg13.693
r_dihedral_angle_4_deg13.099
r_dihedral_angle_1_deg6.847
r_long_range_B_refined5.916
r_long_range_B_other5.913
r_scangle_other3.16
r_scbond_it1.848
r_scbond_other1.848
r_mcangle_other1.666
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.308
r_dihedral_angle_3_deg13.693
r_dihedral_angle_4_deg13.099
r_dihedral_angle_1_deg6.847
r_long_range_B_refined5.916
r_long_range_B_other5.913
r_scangle_other3.16
r_scbond_it1.848
r_scbond_other1.848
r_mcangle_other1.666
r_mcangle_it1.664
r_angle_refined_deg1.125
r_mcbond_it1.016
r_mcbond_other1.006
r_angle_other_deg0.673
r_chiral_restr0.07
r_bond_refined_d0.005
r_gen_planes_refined0.003
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 Atoms968
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling