1XJG

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dATP-UDP complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1XJEpdb entry 1XJE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293PEG8000, sodium acetate, sodium chloride, dithiotreithol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.537α = 90
b = 123.514β = 102.6
c = 105.886γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.803EMBL/DESY, HAMBURGX13

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.52599.90.0621.54.148781
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.52.561000.383.77

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 1XJE2.524.874878126281000.198160.194540.26366RANDOM49.037
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]
6.262.51-2.29-2.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.052
r_dihedral_angle_3_deg19.98
r_dihedral_angle_4_deg18.946
r_dihedral_angle_1_deg7.64
r_scangle_it3.62
r_scbond_it2.389
r_angle_refined_deg1.94
r_mcangle_it1.708
r_mcbond_it0.994
r_metal_ion_refined0.47
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.052
r_dihedral_angle_3_deg19.98
r_dihedral_angle_4_deg18.946
r_dihedral_angle_1_deg7.64
r_scangle_it3.62
r_scbond_it2.389
r_angle_refined_deg1.94
r_mcangle_it1.708
r_mcbond_it0.994
r_metal_ion_refined0.47
r_nbtor_refined0.322
r_symmetry_hbond_refined0.27
r_nbd_refined0.244
r_symmetry_vdw_refined0.229
r_xyhbond_nbd_refined0.177
r_chiral_restr0.136
r_bond_refined_d0.019
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9849
Nucleic Acid Atoms
Solvent Atoms248
Heterogen Atoms112

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling