3GAI

Structure of a F112A variant PduO-type ATP:corrinoid adenosyltransferase from Lactobacillus reuteri complexed with cobalamin and ATP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6298anoxic, 14% PEG 8000, 0.2M potassium chloride, 0.1 M MES, 30 ug/mL E. coli FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydoxycobalamin, 10 mM ATP, 10 mM magnesium chloride, 0.3 M sodium chloride , pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.5251.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.745α = 90
b = 80.745β = 90
c = 89.693γ = 120
Symmetry
Space GroupH 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDSBC-32007-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BMAPS19-BM

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
11.485099.70.05746.2355.636190
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)
11.481.5398.60.12853618

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 DIFFRACTIONTHROUGHOUT1.483036185180499.690.1570.1560.174RANDOM19.396
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]
0.40.20.4-0.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.177
r_dihedral_angle_4_deg16.272
r_dihedral_angle_3_deg11.802
r_dihedral_angle_1_deg4.955
r_scangle_it3.477
r_scbond_it2.342
r_angle_refined_deg2.201
r_mcangle_it1.471
r_mcbond_it0.828
r_nbtor_refined0.316
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.177
r_dihedral_angle_4_deg16.272
r_dihedral_angle_3_deg11.802
r_dihedral_angle_1_deg4.955
r_scangle_it3.477
r_scbond_it2.342
r_angle_refined_deg2.201
r_mcangle_it1.471
r_mcbond_it0.828
r_nbtor_refined0.316
r_chiral_restr0.271
r_nbd_refined0.236
r_symmetry_vdw_refined0.235
r_xyhbond_nbd_refined0.192
r_symmetry_metal_ion_refined0.178
r_symmetry_hbond_refined0.136
r_metal_ion_refined0.134
r_bond_refined_d0.014
r_gen_planes_refined0.01
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1463
Nucleic Acid Atoms
Solvent Atoms159
Heterogen Atoms145

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction