1PEM

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
4.4172.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.079α = 90
b = 99.079β = 90
c = 290.285γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2001-09-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9393ESRFID14-4

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
12.994099.60.1140.11419.114.33004330043
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)
2.993.051000.420.426.6

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.coli2.9919.962843328433151819.960.21870.218780.217540.24297RANDOM55.633
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]
-1.04-1.042.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.818
r_dihedral_angle_1_deg3.82
r_scangle_it2.303
r_angle_refined_deg1.77
r_mcangle_it1.279
r_scbond_it1.232
r_angle_other_deg0.884
r_mcbond_it0.673
r_symmetry_vdw_other0.332
r_nbd_refined0.273
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg19.818
r_dihedral_angle_1_deg3.82
r_scangle_it2.303
r_angle_refined_deg1.77
r_mcangle_it1.279
r_scbond_it1.232
r_angle_other_deg0.884
r_mcbond_it0.673
r_symmetry_vdw_other0.332
r_nbd_refined0.273
r_nbd_other0.251
r_symmetry_vdw_refined0.221
r_xyhbond_nbd_refined0.148
r_symmetry_hbond_refined0.143
r_xyhbond_nbd_other0.111
r_chiral_restr0.094
r_nbtor_other0.061
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5447
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing