3TB9

Structure of Yeast Ribonucleotide Reductase 1 Q288A with AMPPNP and CDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CVUPDB ENTRY 2CVU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72980.1M HEPES pH 7.0, 15-25% PEG 3350, 0.2M NaCl, 10 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0439.62

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.886α = 90
b = 116.959β = 90
c = 64.329γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152011-03-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-E0.98APS24-ID-E

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
12.53501000.105257.92848428484
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)
12.532.591000.51958

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2CVU2.5343.482848425067279399.90.202480.198530.2375RANDOM39.857
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]
-1.49-2.053.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.645
r_dihedral_angle_4_deg19.033
r_dihedral_angle_3_deg18.243
r_dihedral_angle_1_deg6.219
r_scangle_it3.08
r_scbond_it1.944
r_angle_refined_deg1.468
r_mcangle_it1.397
r_mcbond_it0.75
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.645
r_dihedral_angle_4_deg19.033
r_dihedral_angle_3_deg18.243
r_dihedral_angle_1_deg6.219
r_scangle_it3.08
r_scbond_it1.944
r_angle_refined_deg1.468
r_mcangle_it1.397
r_mcbond_it0.75
r_nbtor_refined0.307
r_nbd_refined0.213
r_xyhbond_nbd_refined0.163
r_symmetry_vdw_refined0.155
r_chiral_restr0.105
r_symmetry_hbond_refined0.099
r_bond_refined_d0.012
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 Atoms5107
Nucleic Acid Atoms
Solvent Atoms114
Heterogen Atoms57

Software

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