2NT8

ATP bound at the active site of a PduO type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NOGPDB ENTRY 1NOG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1BATCH8.52930.85 M Ammonium sulfate, 50 mM magnesium chloride, 150 mM sodium chloride, 1.5 mM ATP, 4 mM hydroxocobalamin, pH 8.5, BATCH, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.244.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 110.609α = 90
b = 110.609β = 90
c = 110.609γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-32005-11-21MSINGLE 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
11.685099.40.04611.39.525595
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.681.7499.40.2340.2344.16.82522

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1NOG1.683025595130599.460.1750.1730.204RANDOM23.946
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.427
r_dihedral_angle_4_deg14.683
r_dihedral_angle_3_deg12.146
r_dihedral_angle_1_deg5.209
r_scangle_it3.699
r_scbond_it2.654
r_mcangle_it1.687
r_angle_refined_deg1.341
r_mcbond_it1.056
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.427
r_dihedral_angle_4_deg14.683
r_dihedral_angle_3_deg12.146
r_dihedral_angle_1_deg5.209
r_scangle_it3.699
r_scbond_it2.654
r_mcangle_it1.687
r_angle_refined_deg1.341
r_mcbond_it1.056
r_nbtor_refined0.304
r_nbd_refined0.208
r_symmetry_vdw_refined0.198
r_xyhbond_nbd_refined0.138
r_symmetry_hbond_refined0.134
r_chiral_restr0.084
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1440
Nucleic Acid Atoms
Solvent Atoms141
Heterogen Atoms49

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling