2XND

Crystal structure of bovine F1-c8 sub-complex of ATP Synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E79PDB ENTRY 1E79

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17CRYSTALS WERE GROWN UNDER OIL BY MIXING EQUAL VOLUMES OF PROTEIN (10MG/ML IN 20MM TRIS PH 8.0, 10% GLYCEROL, 1MM ADP, 1MM AMP-PNP, 2MM MGSO4, 0.02% NAN3, 5.7MM TDM) AND PRECIPITANT SOLUTION (50MM HEPES PH 7.0, 14% PEG4600, 50MM K2HPO4)
Crystal Properties
Matthews coefficientSolvent content
3.1761.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 155.74α = 90
b = 157.1β = 90
c = 247.27γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2010-05-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
13.5132.699.60.263.73.67295971.804
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)
13.53.5999.50.821.63.5

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 1E793.5132.672959385599.60.263410.261260.30397RANDOM80.15
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]
-8.211.217
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_3_deg15.871
r_dihedral_angle_4_deg14.088
r_dihedral_angle_1_deg4.632
r_angle_refined_deg0.996
r_scangle_it0.562
r_mcangle_it0.419
r_scbond_it0.314
r_mcbond_it0.229
r_chiral_restr0.059
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.975
r_dihedral_angle_3_deg15.871
r_dihedral_angle_4_deg14.088
r_dihedral_angle_1_deg4.632
r_angle_refined_deg0.996
r_scangle_it0.562
r_mcangle_it0.419
r_scbond_it0.314
r_mcbond_it0.229
r_chiral_restr0.059
r_bond_refined_d0.006
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms28025
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms171

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing