1PEU

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
4.4272.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 98.99α = 90
b = 98.99β = 90
c = 291.488γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Mirror2001-12-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2

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
13.2431000.120.1215.711.12482924829
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)
3.23.311000.380.385.211.44

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.coli3.2432349823498126199.740.20610.20610.203760.251RANDOM40.666
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]
-0.82-0.821.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.742
r_dihedral_angle_1_deg4.59
r_scangle_it3.848
r_scbond_it2.166
r_angle_refined_deg2.048
r_mcangle_it1.736
r_angle_other_deg1.024
r_mcbond_it0.905
r_nbd_refined0.319
r_nbd_other0.283
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg22.742
r_dihedral_angle_1_deg4.59
r_scangle_it3.848
r_scbond_it2.166
r_angle_refined_deg2.048
r_mcangle_it1.736
r_angle_other_deg1.024
r_mcbond_it0.905
r_nbd_refined0.319
r_nbd_other0.283
r_symmetry_vdw_other0.278
r_symmetry_hbond_refined0.26
r_xyhbond_nbd_refined0.202
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_other0.172
r_chiral_restr0.134
r_symmetry_hbond_other0.077
r_bond_refined_d0.023
r_gen_planes_refined0.007
r_nbtor_other0.006
r_gen_planes_other0.003
r_bond_other_d0.002
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5528
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
AMoREphasing