3S87

Structure of Yeast Ribonucleotide Reductase 1 with dGTP and ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CVX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION729820-25% PEG 3350, 0.1 M HEPES, 0.1 M sodium chloride, pH 7.0, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0740.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.618α = 90
b = 117.191β = 90
c = 65.524γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2010-08-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.03APS23-ID-B

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
12.252099.780.07215535900
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)
12.252.3195.40.5852.073.62950

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 DIFFRACTIONIsomorphousTHROUGHOUT2CVX2.252035900402299.780.20990.204250.26062RANDOM45.436
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]
-4.56-0.585.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.332
r_dihedral_angle_4_deg21.781
r_dihedral_angle_3_deg19.075
r_dihedral_angle_1_deg6.444
r_scangle_it3.363
r_scbond_it2.063
r_angle_refined_deg1.58
r_mcangle_it1.385
r_mcbond_it0.741
r_chiral_restr0.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.332
r_dihedral_angle_4_deg21.781
r_dihedral_angle_3_deg19.075
r_dihedral_angle_1_deg6.444
r_scangle_it3.363
r_scbond_it2.063
r_angle_refined_deg1.58
r_mcangle_it1.385
r_mcbond_it0.741
r_chiral_restr0.117
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms5283
Nucleic Acid Atoms
Solvent Atoms202
Heterogen Atoms59

Software

Software
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling