7KOV

Crystal structure of Azotobacter vinelandii 3-mercaptopropionic acid dioxygenase in complex with thiocyanate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6XB9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2940.05 M HEPES pH 7, 44% pentaerythritol propoxylate (5/4 PO/OH), 0.6 M sodium thiocyanate
Crystal Properties
Matthews coefficientSolvent content
2.4349.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 102.182α = 90
b = 102.182β = 90
c = 301.935γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2020-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.979180APS24-ID-E

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
12.955099.90.1850.46812.912.920505
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.953.132.8830.468

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 REPLACEMENTTHROUGHOUT6XB92.9549.8819476102699.780.21620.21490.2411RANDOM97.703
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]
1.780.891.78-5.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.603
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg13.607
r_dihedral_angle_1_deg6.675
r_angle_refined_deg1.223
r_angle_other_deg1.049
r_chiral_restr0.037
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.603
r_dihedral_angle_4_deg16.935
r_dihedral_angle_3_deg13.607
r_dihedral_angle_1_deg6.675
r_angle_refined_deg1.223
r_angle_other_deg1.049
r_chiral_restr0.037
r_bond_refined_d0.003
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6124
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing