2CVS

Structures of Yeast Ribonucleotide Reductase I


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION6.5298PEG 3350, sodium acetate, ammonium sulfate, pH 6.5, EVAPORATION, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0437.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.511α = 90
b = 117.166β = 90
c = 63.362γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2004-06-02MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R1.5418, 0.91900, 0.91940

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
12.65097.60.0720.07220.13.32381823818
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.6998.90.4450.4452.43.13098

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONMADTHROUGHOUT2.65022679254797.760.210710.204360.26693RANDOM51.692
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]
-0.12-3.093.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_3_deg19.012
r_dihedral_angle_4_deg15.267
r_dihedral_angle_1_deg6.148
r_scangle_it2.546
r_scbond_it1.598
r_angle_refined_deg1.47
r_mcangle_it1.419
r_mcbond_it0.791
r_nbtor_refined0.318
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_3_deg19.012
r_dihedral_angle_4_deg15.267
r_dihedral_angle_1_deg6.148
r_scangle_it2.546
r_scbond_it1.598
r_angle_refined_deg1.47
r_mcangle_it1.419
r_mcbond_it0.791
r_nbtor_refined0.318
r_symmetry_vdw_refined0.272
r_nbd_refined0.236
r_xyhbond_nbd_refined0.182
r_chiral_restr0.105
r_symmetry_hbond_refined0.105
r_bond_refined_d0.013
r_gen_planes_refined0.005
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_refined
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 Atoms5254
Nucleic Acid Atoms
Solvent Atoms181
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing