5DAV

Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with 4-Methoxydehydrocyclopeptin


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.1643

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.05α = 90
b = 120.77β = 90
c = 66.66γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2015-06-13MSINGLE 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
11.83099.60.006618.65.12771027599
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)
11.81.999.80.5453.3

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 REPLACEMENTTHROUGHOUT5DAP1.81526218138099.620.166220.16440.19618RANDOM27.146
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]
-1.812.8-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.361
r_sphericity_free25.019
r_dihedral_angle_4_deg15.038
r_dihedral_angle_3_deg12.962
r_sphericity_bonded6.819
r_dihedral_angle_1_deg5.287
r_long_range_B_refined2.406
r_long_range_B_other2.167
r_scangle_other1.373
r_mcangle_it1.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.361
r_sphericity_free25.019
r_dihedral_angle_4_deg15.038
r_dihedral_angle_3_deg12.962
r_sphericity_bonded6.819
r_dihedral_angle_1_deg5.287
r_long_range_B_refined2.406
r_long_range_B_other2.167
r_scangle_other1.373
r_mcangle_it1.34
r_mcangle_other1.339
r_scbond_it1.197
r_scbond_other1.193
r_angle_refined_deg1.045
r_mcbond_it1.003
r_mcbond_other0.999
r_rigid_bond_restr0.866
r_angle_other_deg0.741
r_chiral_restr0.058
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_refined_d0.004
r_bond_other_d0.001
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 Atoms238
Heterogen Atoms35

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing