5OA8

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with demethylated cyclopeptin (1d)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5DAP 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1643.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.09α = 90
b = 120.06β = 90
c = 67.02γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2016-11-20MSINGLE 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
11.755099.30.05416.45.229922
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)
11.751.8599.40.5622.6

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 REPLACEMENTTHROUGHOUT5DAP1.751528366149299.110.160660.156760.19349RANDOM33.727
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]
-0.920.840.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.55
r_sphericity_free25.752
r_dihedral_angle_4_deg14.586
r_dihedral_angle_3_deg12.267
r_sphericity_bonded9.403
r_dihedral_angle_1_deg5.79
r_long_range_B_refined3.036
r_long_range_B_other2.779
r_mcangle_it1.965
r_mcangle_other1.965
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.55
r_sphericity_free25.752
r_dihedral_angle_4_deg14.586
r_dihedral_angle_3_deg12.267
r_sphericity_bonded9.403
r_dihedral_angle_1_deg5.79
r_long_range_B_refined3.036
r_long_range_B_other2.779
r_mcangle_it1.965
r_mcangle_other1.965
r_scangle_other1.807
r_scbond_it1.554
r_scbond_other1.554
r_mcbond_it1.459
r_mcbond_other1.456
r_angle_refined_deg1.256
r_rigid_bond_restr1.205
r_angle_other_deg0.902
r_chiral_restr0.068
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms2228
Nucleic Acid Atoms
Solvent Atoms195
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing