5DAP

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1343

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.11α = 90
b = 117.71β = 90
c = 67.16γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-03-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.73097.50.05616.25.43225231446
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)
11.71.897.90.5113.6

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 REPLACEMENTTHROUGHOUT4NAO1.71529873157397.470.192440.179480.1954RANDOM27.536
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]
-1.743.19-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.302
r_sphericity_free24.235
r_dihedral_angle_4_deg17.934
r_dihedral_angle_3_deg14.96
r_dihedral_angle_1_deg5.78
r_sphericity_bonded4.676
r_long_range_B_refined2.548
r_long_range_B_other2.104
r_mcangle_it1.274
r_mcangle_other1.274
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.302
r_sphericity_free24.235
r_dihedral_angle_4_deg17.934
r_dihedral_angle_3_deg14.96
r_dihedral_angle_1_deg5.78
r_sphericity_bonded4.676
r_long_range_B_refined2.548
r_long_range_B_other2.104
r_mcangle_it1.274
r_mcangle_other1.274
r_scbond_it1.272
r_scbond_other1.272
r_scangle_other1.2
r_angle_refined_deg1.091
r_mcbond_it1.074
r_mcbond_other1.073
r_rigid_bond_restr1
r_angle_other_deg0.749
r_chiral_restr0.064
r_bond_refined_d0.005
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2227
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms11

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing