1XJF

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RLRPDB entry 1RLR

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
2.5555

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.3α = 90
b = 123.76β = 103.82
c = 107.03γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2002-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.076MAX 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
12.42599.30.06312.13.7557137
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)
2.42.699.50.3883.2

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 1RLR2.422.8854368293599.750.211050.208360.26026RANDOM46.783
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]
-0.11-0.060.060.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.996
r_dihedral_angle_4_deg22.55
r_dihedral_angle_3_deg18.675
r_dihedral_angle_1_deg6.871
r_scangle_it3.441
r_scbond_it2.115
r_angle_refined_deg1.651
r_mcangle_it1.57
r_mcbond_it0.883
r_metal_ion_refined0.572
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.996
r_dihedral_angle_4_deg22.55
r_dihedral_angle_3_deg18.675
r_dihedral_angle_1_deg6.871
r_scangle_it3.441
r_scbond_it2.115
r_angle_refined_deg1.651
r_mcangle_it1.57
r_mcbond_it0.883
r_metal_ion_refined0.572
r_symmetry_hbond_refined0.313
r_nbtor_refined0.308
r_symmetry_vdw_refined0.252
r_nbd_refined0.221
r_xyhbond_nbd_refined0.174
r_chiral_restr0.108
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms9878
Nucleic Acid Atoms
Solvent Atoms254
Heterogen Atoms62

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
CCP4data scaling
CNSphasing