7OLM

Dioxygenase AsqJ mutant (V72I) in complex with 2b-O-O and Tris


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293100 mM TRIS/HCl, 1 M LiBr, 26% PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.1743.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.21α = 90
b = 121.06β = 90
c = 66.73γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-07MSINGLE 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
11.753098.10.068134.129723
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)
11.751.8595.30.5082.9

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 REPLACEMENTTHROUGHOUT5DAP1.753028229148698.090.17590.17450.2035RANDOM26.878
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]
-0.421.07-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.892
r_dihedral_angle_4_deg12.422
r_dihedral_angle_3_deg11.186
r_dihedral_angle_1_deg6.609
r_angle_refined_deg1.208
r_angle_other_deg1.095
r_rigid_bond_restr0.248
r_chiral_restr0.043
r_gen_planes_other0.006
r_gen_planes_refined0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.892
r_dihedral_angle_4_deg12.422
r_dihedral_angle_3_deg11.186
r_dihedral_angle_1_deg6.609
r_angle_refined_deg1.208
r_angle_other_deg1.095
r_rigid_bond_restr0.248
r_chiral_restr0.043
r_gen_planes_other0.006
r_gen_planes_refined0.005
r_bond_refined_d0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2228
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing