2D7D

Structural insights into the cryptic DNA dependent ATP-ase activity of UvrB


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1D9XPDB entry 1D9X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.528918-20% (w/v) PEG 10000 0.1M Tris-Hcl, pH 8.5, Microbatch, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1241.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.231α = 90
b = 98.215β = 90
c = 95.405γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMirrors2005-04-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.976ESRFBM14

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
12.13096.10.0820.0825.85.839593395932.42.425
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)
2.12.2192.90.310.312.45.85487

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 1D9X2.1303959339593195396.10.229610.229610.226790.28485RANDOM23.146
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]
2.03-0.85-1.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.976
r_dihedral_angle_4_deg19.562
r_dihedral_angle_3_deg18.419
r_dihedral_angle_1_deg6.34
r_scangle_it3.396
r_scbond_it2.21
r_angle_refined_deg1.61
r_mcangle_it1.273
r_mcbond_it0.78
r_symmetry_hbond_refined0.321
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.976
r_dihedral_angle_4_deg19.562
r_dihedral_angle_3_deg18.419
r_dihedral_angle_1_deg6.34
r_scangle_it3.396
r_scbond_it2.21
r_angle_refined_deg1.61
r_mcangle_it1.273
r_mcbond_it0.78
r_symmetry_hbond_refined0.321
r_nbtor_refined0.304
r_symmetry_vdw_refined0.273
r_nbd_refined0.219
r_xyhbond_nbd_refined0.178
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5199
Nucleic Acid Atoms61
Solvent Atoms204
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing