2IDX

Structure of Human ATP:Cobalamin adenosyltransferase bound to ATP.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RTY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29820% PEG 3350, 0.2 M MgSO4, 10% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.1761.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.238α = 90
b = 111.238β = 90
c = 115.526γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2005-08-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X26C1.0NSLSX26C

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
12.5501000.136929063-246.2
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)
2.52.591000.5622884

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 REPLACEMENTTHROUGHOUT1RTY2.530287651428990.20.1970.251RANDOM34.397
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]
0.560.280.56-0.84
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.842
r_dihedral_angle_4_deg23.445
r_dihedral_angle_3_deg18.251
r_dihedral_angle_1_deg6.068
r_scangle_it2.88
r_scbond_it1.849
r_angle_refined_deg1.484
r_mcangle_it1.342
r_mcbond_it0.786
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.842
r_dihedral_angle_4_deg23.445
r_dihedral_angle_3_deg18.251
r_dihedral_angle_1_deg6.068
r_scangle_it2.88
r_scbond_it1.849
r_angle_refined_deg1.484
r_mcangle_it1.342
r_mcbond_it0.786
r_nbtor_refined0.312
r_symmetry_hbond_refined0.241
r_nbd_refined0.223
r_xyhbond_nbd_refined0.163
r_symmetry_vdw_refined0.162
r_metal_ion_refined0.102
r_chiral_restr0.095
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3990
Nucleic Acid Atoms
Solvent Atoms171
Heterogen Atoms82

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction