2R9V

Crystal structure of ATP synthase subunit alpha (TM1612) from Thermotoga maritima at 2.10 A resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.21277NANODROP, 1.3% PEG 6000, 0.1M Citric acid pH 4.21, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
4.4872.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 97.41α = 90
b = 97.41β = 90
c = 219.38γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-08-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.2.20.97960ALS8.2.2

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
12.148.67999.80.14311.447.1762330-327.14
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)
12.12.1999.80.89727.29

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 DIFFRACTIONSADTHROUGHOUT2.148.67962319317699.770.1820.180.215RANDOM29.378
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]
1.621.62-3.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.171
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg13.231
r_scangle_it5.39
r_dihedral_angle_1_deg4.831
r_scbond_it4.311
r_mcangle_it3.365
r_mcbond_it2.401
r_angle_refined_deg1.644
r_angle_other_deg0.978
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.171
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg13.231
r_scangle_it5.39
r_dihedral_angle_1_deg4.831
r_scbond_it4.311
r_mcangle_it3.365
r_mcbond_it2.401
r_angle_refined_deg1.644
r_angle_other_deg0.978
r_mcbond_other0.521
r_symmetry_vdw_refined0.31
r_symmetry_vdw_other0.285
r_nbd_refined0.22
r_nbd_other0.201
r_symmetry_hbond_refined0.196
r_nbtor_refined0.18
r_xyhbond_nbd_refined0.156
r_chiral_restr0.099
r_nbtor_other0.088
r_bond_refined_d0.017
r_metal_ion_refined0.009
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3802
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
PHENIXrefinement
SHELXphasing
MolProbitymodel building
XSCALEdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
SHARPphasing