1UZR

Crystal Structure of the Class Ib Ribonucleotide Reductase R2F-2 subunit from Mycobacterium tuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1R2FPDB ENTRY 1R2F

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.60.6 M AMSO4, 100MM NACT PH 5.6, 50MM NA/K TARTRATE
Crystal Properties
Matthews coefficientSolvent content
3.463.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 161.492α = 90
b = 161.492β = 90
c = 115.53γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
12.240990.091104.8477125
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)
12.22.2593.50.4451.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 1R2F2.2111.873204387098.90.1770.1750.202RANDOM28.39
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]
-0.55-0.551.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.974
r_scangle_it5.35
r_scbond_it3.191
r_mcangle_it1.947
r_angle_refined_deg1.85
r_mcbond_it1.013
r_angle_other_deg0.973
r_symmetry_vdw_other0.355
r_nbd_other0.234
r_nbd_refined0.232
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.974
r_scangle_it5.35
r_scbond_it3.191
r_mcangle_it1.947
r_angle_refined_deg1.85
r_mcbond_it1.013
r_angle_other_deg0.973
r_symmetry_vdw_other0.355
r_nbd_other0.234
r_nbd_refined0.232
r_symmetry_hbond_refined0.197
r_xyhbond_nbd_refined0.166
r_symmetry_vdw_refined0.132
r_chiral_restr0.12
r_nbtor_other0.094
r_metal_ion_refined0.077
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_gen_planes_other0.008
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_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 Atoms6905
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms63

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing