6BLB

1.88 Angstrom Resolution Crystal Structure Holliday Junction ATP-dependent DNA Helicase (RuvB) from Pseudomonas aeruginosa in Complex with ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IN4PDB entry 1IN4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72958.6 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3, screen: Classics II (D3), 0.1 M HEPES, pH 7.0, 30% v/v Jeffamine ED-2001
Crystal Properties
Matthews coefficientSolvent content
2.0439.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.537α = 90
b = 85.537β = 90
c = 77.103γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDC(111)2017-06-20MSINGLE 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)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.88301000.0760.0760.0810.02826.98.426154-326.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.881.911000.7970.7970.8490.2910.8112.98.3

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 1IN41.8828.6424830129599.940.174520.172470.21307RANDOM32.916
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]
0.030.010.03-0.09
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.499
r_dihedral_angle_4_deg12.19
r_dihedral_angle_3_deg11.697
r_long_range_B_refined5.279
r_long_range_B_other5.137
r_scangle_other3.008
r_dihedral_angle_1_deg2.964
r_mcangle_it1.852
r_mcangle_other1.851
r_scbond_it1.847
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.499
r_dihedral_angle_4_deg12.19
r_dihedral_angle_3_deg11.697
r_long_range_B_refined5.279
r_long_range_B_other5.137
r_scangle_other3.008
r_dihedral_angle_1_deg2.964
r_mcangle_it1.852
r_mcangle_other1.851
r_scbond_it1.847
r_scbond_other1.846
r_angle_refined_deg1.369
r_mcbond_it1.209
r_mcbond_other1.208
r_angle_other_deg0.868
r_chiral_restr0.081
r_gen_planes_refined0.022
r_gen_planes_other0.018
r_bond_refined_d0.009
r_bond_other_d0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2430
Nucleic Acid Atoms
Solvent Atoms191
Heterogen Atoms37

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing