2C2P

The crystal structure of mismatch specific uracil-DNA glycosylase (MUG) from Deinococcus radiodurans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1MUGPDB ENTRY 1MUG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M SODIUM CACODYLATE PH 6.5, 30% W/V PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.651.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.733α = 90
b = 101.733β = 90
c = 37.561γ = 120
Symmetry
Space GroupP 6

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2003-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.751299.90.0518.85.322686
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)
11.751.841000.532.85.1

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 1MUG1.7587.7120611207199.90.1830.1790.22RANDOM23.13
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]
0.580.290.58-0.87
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.308
r_scangle_it5.034
r_scbond_it3.183
r_mcangle_it2.298
r_angle_refined_deg1.916
r_mcbond_it1.341
r_angle_other_deg1.047
r_symmetry_vdw_other0.309
r_nbd_other0.254
r_nbd_refined0.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg7.308
r_scangle_it5.034
r_scbond_it3.183
r_mcangle_it2.298
r_angle_refined_deg1.916
r_mcbond_it1.341
r_angle_other_deg1.047
r_symmetry_vdw_other0.309
r_nbd_other0.254
r_nbd_refined0.23
r_xyhbond_nbd_refined0.171
r_symmetry_vdw_refined0.159
r_symmetry_hbond_refined0.138
r_chiral_restr0.128
r_nbtor_other0.085
r_bond_refined_d0.021
r_gen_planes_refined0.009
r_gen_planes_other0.003
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_refined
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 Atoms1426
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms4

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing