1YCE | pdb_00001yce

Structure of the rotor ring of F-type Na+-ATPase from Ilyobacter tartaricus


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION4.529015% PEG400, 0.1M NaAc, pH 4.5, VAPOR DIFFUSION, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.565

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 147.7α = 90
b = 140β = 118.4
c = 153γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-02-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9756ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.4100.1830.1751010209310198822
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.595.20.6350.5893.38

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONTHROUGHOUT2.4101988221046199.430.202820.200550.210.245950.25RANDOM44.851
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]
-4.091.352.772.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.786
r_dihedral_angle_4_deg23.67
r_dihedral_angle_3_deg17.467
r_dihedral_angle_1_deg6.157
r_scangle_it3.68
r_scbond_it2.255
r_angle_refined_deg1.91
r_mcangle_it1.257
r_angle_other_deg1.005
r_mcbond_it0.717
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.786
r_dihedral_angle_4_deg23.67
r_dihedral_angle_3_deg17.467
r_dihedral_angle_1_deg6.157
r_scangle_it3.68
r_scbond_it2.255
r_angle_refined_deg1.91
r_mcangle_it1.257
r_angle_other_deg1.005
r_mcbond_it0.717
r_symmetry_vdw_other0.264
r_nbd_refined0.248
r_symmetry_vdw_refined0.237
r_symmetry_hbond_refined0.223
r_mcbond_other0.214
r_nbtor_refined0.181
r_xyhbond_nbd_refined0.175
r_nbd_other0.171
r_metal_ion_refined0.148
r_chiral_restr0.112
r_nbtor_other0.091
r_bond_refined_d0.021
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms27104
Nucleic Acid Atoms
Solvent Atoms513
Heterogen Atoms484

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHASERphasing