6MP9

X-ray crystal structure of VioC bound to Fe(II), 2-oxo-5-guanidinopentanoic acid, and succinate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.5293succinate, TRIS-HCl
Crystal Properties
Matthews coefficientSolvent content
2.1542.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.676α = 90
b = 66.94β = 109.12
c = 62.856γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2017-02-11MSINGLE 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
11.959.3997.70.060.070.0369.23.724739
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)
11.91.9384.10.4710.5570.2930.8643.4

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 DIFFRACTIONTHROUGHOUT1.8959.3921145115487.770.19440.19340.2117RANDOM21.709
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]
0.31-0.47-0.280.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.359
r_dihedral_angle_3_deg12.403
r_dihedral_angle_4_deg11.577
r_dihedral_angle_1_deg5.48
r_angle_refined_deg1.036
r_angle_other_deg0.714
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.359
r_dihedral_angle_3_deg12.403
r_dihedral_angle_4_deg11.577
r_dihedral_angle_1_deg5.48
r_angle_refined_deg1.036
r_angle_other_deg0.714
r_chiral_restr0.056
r_bond_refined_d0.005
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 Atoms2602
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms21

Software

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