3EIU

A second transient position of ATP on its trail to the nucleotide-binding site of subunit B of the motor protein A1Ao ATP synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C61PDB ENTRY 2C61

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP529115% glycerol, 20% PEG 400, 2mM Mg2+ ATP, 0.1M Sodium Chloride, 0.1M Sodium citrate (pH 5.0), vapor diffusion,sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.346.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.693α = 90
b = 96.867β = 90
c = 129.631γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-07-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.00NSRRCBL13B1

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
13.430910.1678.4933.5132921205578.55
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)
13.43.5285.70.4731.942.41094

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C613.4324.62114331203259590.520.3080.2490.2460.315RANDOM72.12
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]
0.18-0.01-0.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.391
r_dihedral_angle_3_deg20.034
r_dihedral_angle_4_deg13.04
r_dihedral_angle_1_deg5.199
r_angle_refined_deg0.997
r_mcangle_it0.421
r_scangle_it0.417
r_nbtor_refined0.299
r_scbond_it0.244
r_mcbond_it0.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.391
r_dihedral_angle_3_deg20.034
r_dihedral_angle_4_deg13.04
r_dihedral_angle_1_deg5.199
r_angle_refined_deg0.997
r_mcangle_it0.421
r_scangle_it0.417
r_nbtor_refined0.299
r_scbond_it0.244
r_mcbond_it0.233
r_nbd_refined0.187
r_symmetry_vdw_refined0.179
r_xyhbond_nbd_refined0.126
r_symmetry_hbond_refined0.097
r_chiral_restr0.067
r_bond_refined_d0.006
r_gen_planes_refined0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6506
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms44

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling