1PEQ

Ribonucleotide Reductase Protein R1E from Salmonella typhimurium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RLRpoly-alanin model of ribonucleotide reductase protein R1 from E.coli

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.2288sodium malonate, magnesium chloride, DTT, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
4.4172.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.144α = 90
b = 99.144β = 90
c = 289.544γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-07-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.9393ESRFID14-1

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
12.84099.10.0790.07918.37.943637136371
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)
2.82.8599.10.2860.2865.5

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpoly-alanin model of ribonucleotide reductase protein R1 from E.coli2.8403453634536181599.260.21660.21660.215070.2464RANDOM48.589
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.961
r_scangle_it4.397
r_dihedral_angle_1_deg3.373
r_scbond_it2.564
r_angle_refined_deg1.931
r_mcangle_it1.92
r_mcbond_it1.013
r_angle_other_deg0.926
r_nbd_refined0.271
r_symmetry_vdw_other0.234
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg16.961
r_scangle_it4.397
r_dihedral_angle_1_deg3.373
r_scbond_it2.564
r_angle_refined_deg1.931
r_mcangle_it1.92
r_mcbond_it1.013
r_angle_other_deg0.926
r_nbd_refined0.271
r_symmetry_vdw_other0.234
r_nbd_other0.227
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.138
r_chiral_restr0.108
r_symmetry_hbond_refined0.093
r_xyhbond_nbd_other0.083
r_bond_refined_d0.023
r_gen_planes_refined0.008
r_gen_planes_other0.003
r_bond_other_d0.001
r_nbtor_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5423
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing