2XAK

Ribonucleotide reductase Y730NO2Y 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
3.0554

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 224.091α = 90
b = 224.091β = 90
c = 337.157γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2009-01-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.867.271000.1416.179.7179929-3.7
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)
12.82.821000.643.358.41

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 2X0X2.8169.031279929401199.9820.1810.17810.2408RANDOM36.914
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]
0.2750.1370.275-0.412
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.475
r_dihedral_angle_3_deg19.036
r_dihedral_angle_4_deg18.925
r_dihedral_angle_1_deg6.153
r_scangle_it2.347
r_scbond_it1.358
r_angle_refined_deg1.327
r_mcangle_it1.098
r_mcbond_it0.607
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.475
r_dihedral_angle_3_deg19.036
r_dihedral_angle_4_deg18.925
r_dihedral_angle_1_deg6.153
r_scangle_it2.347
r_scbond_it1.358
r_angle_refined_deg1.327
r_mcangle_it1.098
r_mcbond_it0.607
r_nbtor_refined0.31
r_symmetry_hbond_refined0.299
r_nbd_refined0.219
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.159
r_chiral_restr0.094
r_bond_refined_d0.01
r_gen_planes_refined0.004
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 Atoms17835
Nucleic Acid Atoms
Solvent Atoms439
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
TRUNCATEdata scaling
REFMACphasing