4YXW

Bovine heart mitochondrial F1-ATPase inhibited by AMP-PNP and ADP in the presence of thiophosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2CK3 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICRODIALYSIS8.2295PEG 6000, sodium chloride, magnesium chloride, Tris-HCl, AMP-PNP, ADP, sodium monothiophosphate
Crystal Properties
Matthews coefficientSolvent content
2.2745.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.353α = 90
b = 123.052β = 90
c = 261.276γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-08-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.979DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
13.176.5295.40.1710.1230.8846.42.65918653.48
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.13.1896.10.6490.4590.5472.22.74360

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 REPLACEMENTTHROUGHOUT2CK33.176.555823300094.190.22870.22630.2734RANDOM75.741
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]
-1.31-0.11.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.133
r_dihedral_angle_3_deg11.832
r_dihedral_angle_4_deg11.145
r_dihedral_angle_1_deg5.158
r_mcangle_it2.46
r_mcbond_it1.376
r_mcbond_other1.376
r_angle_refined_deg1.038
r_angle_other_deg0.837
r_chiral_restr0.055
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.133
r_dihedral_angle_3_deg11.832
r_dihedral_angle_4_deg11.145
r_dihedral_angle_1_deg5.158
r_mcangle_it2.46
r_mcbond_it1.376
r_mcbond_other1.376
r_angle_refined_deg1.038
r_angle_other_deg0.837
r_chiral_restr0.055
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24623
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms167

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction