5DAX

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with demethylated cyclopeptin


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
2.1443

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.29α = 90
b = 118.05β = 90
c = 67.31γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-03-072015-03-07MSINGLE 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
11.73097.90.04120.85.33249031808
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)
11.71.898.30.4353.4

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 REPLACEMENTTHROUGHOUT5DAP1.71530216159197.880.181750.180660.19859RANDOM31.521
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]
-2.183.43-1.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.075
r_sphericity_free22.85
r_dihedral_angle_4_deg20.536
r_dihedral_angle_3_deg15.108
r_dihedral_angle_1_deg5.877
r_sphericity_bonded5.043
r_long_range_B_refined2.952
r_long_range_B_other2.581
r_scbond_it1.707
r_scbond_other1.707
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.075
r_sphericity_free22.85
r_dihedral_angle_4_deg20.536
r_dihedral_angle_3_deg15.108
r_dihedral_angle_1_deg5.877
r_sphericity_bonded5.043
r_long_range_B_refined2.952
r_long_range_B_other2.581
r_scbond_it1.707
r_scbond_other1.707
r_rigid_bond_restr1.636
r_mcangle_it1.559
r_mcangle_other1.558
r_scangle_other1.554
r_mcbond_it1.293
r_mcbond_other1.293
r_angle_refined_deg1.178
r_angle_other_deg0.792
r_chiral_restr0.07
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d0.002
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 Atoms265
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing