2NMV

Damage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2D7DPDB ENTRY 2D7D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.528918-20% PEG 20000, 0.1M pH 8.5 Tris-Hcl, microbatch, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1141.74

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.41α = 90
b = 95.597β = 90
c = 97.878γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Bent cylindrical mirror2005-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.980ESRFID23-2

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
12.9568.3699.10.0940.09415.95.3151092273.7
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)
2.953.0399.30.3690.3695.25.51087

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2D7D2.9568.36151091430975598.830.227060.227060.224280.28074RANDOM48.348
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]
1.21-2.040.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.008
r_dihedral_angle_3_deg20.405
r_dihedral_angle_4_deg18.861
r_dihedral_angle_1_deg6.527
r_scangle_it3.052
r_scbond_it1.799
r_angle_refined_deg1.713
r_mcangle_it1.234
r_mcbond_it0.696
r_nbtor_refined0.323
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.008
r_dihedral_angle_3_deg20.405
r_dihedral_angle_4_deg18.861
r_dihedral_angle_1_deg6.527
r_scangle_it3.052
r_scbond_it1.799
r_angle_refined_deg1.713
r_mcangle_it1.234
r_mcbond_it0.696
r_nbtor_refined0.323
r_nbd_refined0.246
r_symmetry_vdw_refined0.243
r_symmetry_hbond_refined0.181
r_xyhbond_nbd_refined0.169
r_chiral_restr0.101
r_bond_refined_d0.016
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5179
Nucleic Acid Atoms84
Solvent Atoms
Heterogen Atoms48

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing