3AOU

Structure of the Na+ unbound rotor ring modified with N,N f-Dicyclohexylcarbodiimide of the Na+-transporting V-ATPase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DB4PDB ENTRY 2DB4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293100mM Tris-HCl pH7.5, 4% Glycerol, 240mM potassium citrate, 35% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
4.8274.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 120.41α = 90
b = 124.937β = 90
c = 208.221γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152009-10-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1SPring-8BL41XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
13.1448.7993.8553865192911
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)
13.143.3194.80.6710.6711.93.77587

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2DB43.1448.7949285264493.80.21080.208810.24818RANDOM71.158
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]
-6.883.493.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.255
r_dihedral_angle_3_deg18.61
r_dihedral_angle_1_deg5.018
r_scangle_it2.114
r_angle_refined_deg1.391
r_scbond_it1.198
r_mcangle_it0.802
r_mcbond_it0.426
r_chiral_restr0.103
r_bond_refined_d0.011
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.255
r_dihedral_angle_3_deg18.61
r_dihedral_angle_1_deg5.018
r_scangle_it2.114
r_angle_refined_deg1.391
r_scbond_it1.198
r_mcangle_it0.802
r_mcbond_it0.426
r_chiral_restr0.103
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms11270
Nucleic Acid Atoms
Solvent Atoms6
Heterogen Atoms228

Software

Software
Software NamePurpose
BSSdata collection
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling