5DN6

ATP synthase from Paracoccus denitrificans


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829850 mM Tris-HCl pH 8.0, 70-100 mM MgCl2, 18-20% polyethylene glycol 4000
Crystal Properties
Matthews coefficientSolvent content
3.2862.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.001α = 90
b = 187.943β = 97.44
c = 164.724γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-03-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.917DiamondI04-1

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
13.9736.8498.30.2537.79.557347
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)
13.974.0887.91.6041.98.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT3.9836.8454496279198.630.296860.295460.32414RANDOM144.21
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]
-4.49-6.621.484.58
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.273
r_dihedral_angle_3_deg16.225
r_dihedral_angle_4_deg14.222
r_long_range_B_refined13.263
r_long_range_B_other13.263
r_mcangle_it5.476
r_mcangle_other5.476
r_dihedral_angle_1_deg4.898
r_scangle_other3.848
r_mcbond_it3.088
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.273
r_dihedral_angle_3_deg16.225
r_dihedral_angle_4_deg14.222
r_long_range_B_refined13.263
r_long_range_B_other13.263
r_mcangle_it5.476
r_mcangle_other5.476
r_dihedral_angle_1_deg4.898
r_scangle_other3.848
r_mcbond_it3.088
r_mcbond_other3.088
r_scbond_it1.956
r_scbond_other1.956
r_angle_refined_deg1.166
r_angle_other_deg0.962
r_chiral_restr0.067
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.003
r_gen_planes_other0.002
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 Atoms31374
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms156

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PHASERphasing