3S8B

Structure of Yeast Ribonucleotide Reductase 1 with AMPPNP and CDP


X-RAY DIFFRACTION

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
2.0740.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.869α = 90
b = 117.567β = 90
c = 64.967γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-03-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.98APS24-ID-C

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
12.849.0398.760.1312.53.42121218651
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)
12.82.87970.522.83.4

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 DIFFRACTIONIsomorphousTHROUGHOUT2.849.0318651208398.760.212890.208650.25027RANDOM47.421
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]
-0.15-0.020.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.153
r_dihedral_angle_3_deg19.135
r_dihedral_angle_4_deg18.837
r_dihedral_angle_1_deg6.11
r_scangle_it1.897
r_scbond_it1.296
r_angle_refined_deg1.27
r_mcangle_it0.926
r_mcbond_it0.731
r_nbtor_refined0.305
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.153
r_dihedral_angle_3_deg19.135
r_dihedral_angle_4_deg18.837
r_dihedral_angle_1_deg6.11
r_scangle_it1.897
r_scbond_it1.296
r_angle_refined_deg1.27
r_mcangle_it0.926
r_mcbond_it0.731
r_nbtor_refined0.305
r_nbd_refined0.204
r_symmetry_vdw_refined0.178
r_xyhbond_nbd_refined0.144
r_chiral_restr0.094
r_symmetry_hbond_refined0.028
r_metal_ion_refined0.025
r_bond_refined_d0.01
r_gen_planes_refined0.003
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 Atoms5223
Nucleic Acid Atoms
Solvent Atoms42
Heterogen Atoms57

Software

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