6DAX

X-ray crystal structure of VioC bound to Fe(II), L-homoarginine, and 2-oxoglutarate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.52932-oxoglutarate, Tris-HCl
Crystal Properties
Matthews coefficientSolvent content
2.1342.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.376α = 90
b = 67.076β = 108.72
c = 62.646γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2015-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.979APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.75097.20.0540.0630.03311.33.633837
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7386.70.4320.5120.2720.893.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.75032080169396.710.21610.21570.2238RANDOM26.603
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]
1.98-3.43-0.680.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.394
r_dihedral_angle_4_deg13.891
r_dihedral_angle_3_deg11.937
r_dihedral_angle_1_deg5.318
r_angle_refined_deg0.991
r_angle_other_deg0.805
r_chiral_restr0.055
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_refined0.003
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.394
r_dihedral_angle_4_deg13.891
r_dihedral_angle_3_deg11.937
r_dihedral_angle_1_deg5.318
r_angle_refined_deg0.991
r_angle_other_deg0.805
r_chiral_restr0.055
r_bond_refined_d0.005
r_bond_other_d0.003
r_gen_planes_refined0.003
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2647
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms24

Software

Software
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing