3PFI

2.7 Angstrom resolution crystal structure of a probable holliday junction DNA helicase (ruvB) from Campylobacter jejuni subsp. jejuni NCTC 11168 in complex with adenosine-5'-diphosphate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.5295Crystallization condition: Tacsimate 5%, PEG5KMME 10%, B-Tr 0.1M pH 5.5, AMPPNP 10mM. Cryo condition: 30% PEG 5KMME, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
2.856.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.482α = 90
b = 111.482β = 90
c = 355.089γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBe Lenses/Diamond Laue Mono2010-06-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
12.695301000.08616.324.62393123883-3
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)
2.6952.751000.4893.444.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.69529.592264922649123499.820.224270.221910.26796RANDOM67.632
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]
-6.75-3.37-6.7510.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.006
r_dihedral_angle_4_deg9.823
r_dihedral_angle_3_deg8.317
r_scangle_it6.735
r_scbond_it4.327
r_mcangle_it2.404
r_dihedral_angle_1_deg1.601
r_mcbond_it1.306
r_angle_refined_deg1.033
r_angle_other_deg0.705
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg20.006
r_dihedral_angle_4_deg9.823
r_dihedral_angle_3_deg8.317
r_scangle_it6.735
r_scbond_it4.327
r_mcangle_it2.404
r_dihedral_angle_1_deg1.601
r_mcbond_it1.306
r_angle_refined_deg1.033
r_angle_other_deg0.705
r_mcbond_other0.309
r_chiral_restr0.06
r_bond_refined_d0.005
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4541
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms54

Software

Software
Software NamePurpose
Blu-Icedata collection
PHENIXmodel building
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing