1XJJ

Structural mechanism of allosteric substrate specificity in a ribonucleotide reductase: dGTP 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
2.6355

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.07α = 90
b = 123.88β = 103.7
c = 106.3γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7110.964MAX III711

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
11.864299.80.06612.25.2124318124131
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)
1.8621000.43.44.2

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 1XJE1.8642.26117911621799.890.19850.196240.24066RANDOM32.72
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]
1.381.15-0.01-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg18.569
r_dihedral_angle_3_deg17.267
r_dihedral_angle_1_deg6.784
r_scangle_it4.281
r_scbond_it2.849
r_mcangle_it1.882
r_angle_refined_deg1.799
r_mcbond_it1.169
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.765
r_dihedral_angle_4_deg18.569
r_dihedral_angle_3_deg17.267
r_dihedral_angle_1_deg6.784
r_scangle_it4.281
r_scbond_it2.849
r_mcangle_it1.882
r_angle_refined_deg1.799
r_mcbond_it1.169
r_nbtor_refined0.315
r_nbd_refined0.215
r_symmetry_hbond_refined0.201
r_symmetry_vdw_refined0.165
r_xyhbond_nbd_refined0.155
r_metal_ion_refined0.154
r_chiral_restr0.128
r_bond_refined_d0.018
r_gen_planes_refined0.008
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 Atoms9915
Nucleic Acid Atoms
Solvent Atoms550
Heterogen Atoms126

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
XDSdata scaling