2XAV

Ribonucleotide reductase Y731NO2Y and Y730F modified R1 subunit of E. coli


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2X0XPDB ENTRY 2X0X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16LITHIUM SULPHATE 1.5M, SODIUM CHLORIDE BUFFER PH 6.
Crystal Properties
Matthews coefficientSolvent content
3.1654

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 224.664α = 90
b = 224.664β = 90
c = 336.361γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2009-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.884.2193.70.1512.935.9775099-3.7
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)
12.82.8296.80.582.35.54

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2X0X2.8169.031275098378893.70.1730.16870.2473RANDOM41.358
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]
0.1850.0920.185-0.277
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.732
r_dihedral_angle_3_deg20.088
r_dihedral_angle_4_deg19.1
r_dihedral_angle_1_deg6.739
r_scangle_it2.997
r_scbond_it1.829
r_angle_refined_deg1.596
r_mcangle_it1.36
r_mcbond_it0.752
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.732
r_dihedral_angle_3_deg20.088
r_dihedral_angle_4_deg19.1
r_dihedral_angle_1_deg6.739
r_scangle_it2.997
r_scbond_it1.829
r_angle_refined_deg1.596
r_mcangle_it1.36
r_mcbond_it0.752
r_nbtor_refined0.315
r_symmetry_hbond_refined0.279
r_nbd_refined0.241
r_symmetry_vdw_refined0.228
r_xyhbond_nbd_refined0.181
r_chiral_restr0.108
r_bond_refined_d0.015
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17832
Nucleic Acid Atoms
Solvent Atoms627
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
TRUNCATEdata scaling