1XJE

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dTTP-GDP complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R1Rpdb entry 1R1R

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
2.6353.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.391α = 90
b = 124.376β = 103.68
c = 107.243γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-08-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.811EMBL/DESY, HAMBURGX11

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
11.91897.20.0712.232.7119507
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)
11.91.9796.60.3993.2

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 1R1R1.918110169579497.160.184450.182410.22268RANDOM31.972
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]
1.961.30.4-1.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.73
r_dihedral_angle_4_deg19.657
r_dihedral_angle_3_deg16.342
r_dihedral_angle_1_deg6.898
r_scangle_it3.66
r_scbond_it2.633
r_angle_refined_deg1.78
r_mcangle_it1.595
r_mcbond_it1.375
r_angle_other_deg0.948
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.73
r_dihedral_angle_4_deg19.657
r_dihedral_angle_3_deg16.342
r_dihedral_angle_1_deg6.898
r_scangle_it3.66
r_scbond_it2.633
r_angle_refined_deg1.78
r_mcangle_it1.595
r_mcbond_it1.375
r_angle_other_deg0.948
r_symmetry_vdw_other0.337
r_symmetry_vdw_refined0.275
r_mcbond_other0.267
r_nbd_refined0.221
r_nbd_other0.187
r_symmetry_hbond_refined0.185
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.165
r_metal_ion_refined0.133
r_chiral_restr0.125
r_nbtor_other0.089
r_bond_refined_d0.019
r_xyhbond_nbd_other0.018
r_gen_planes_refined0.007
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10001
Nucleic Acid Atoms
Solvent Atoms791
Heterogen Atoms122

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
SCALEPACKdata scaling