2RKW

Intermediate position of ATP on its trail to the binding pocket inside the subunit B mutant R416W of the energy converter 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, 0.1M Sodium Chloride, 0.1M Sodium citrate (pH 5.0), VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2144.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.052α = 90
b = 96.094β = 90
c = 129.941γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315mirrors2007-01-09MSINGLE 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
12.850870.138.45.920054
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)
2.82.960.60.3954.8

Refinement

Statistics
Diffraction IDStructure Solution MethodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTPDB ENTRY 2C612.8134.7319988103386.90.2740.2710.3379.45
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]
0.140.11-0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.656
r_dihedral_angle_3_deg21.035
r_dihedral_angle_4_deg14.095
r_dihedral_angle_1_deg7.295
r_angle_refined_deg1.36
r_scangle_it0.894
r_mcangle_it0.609
r_scbond_it0.537
r_mcbond_it0.335
r_nbtor_refined0.31
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.656
r_dihedral_angle_3_deg21.035
r_dihedral_angle_4_deg14.095
r_dihedral_angle_1_deg7.295
r_angle_refined_deg1.36
r_scangle_it0.894
r_mcangle_it0.609
r_scbond_it0.537
r_mcbond_it0.335
r_nbtor_refined0.31
r_nbd_refined0.235
r_symmetry_vdw_refined0.202
r_xyhbond_nbd_refined0.184
r_chiral_restr0.103
r_symmetry_hbond_refined0.028
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6512
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
REFMACrefinement