3VR3

Crystal structure of AMP-PNP bound A3B3 complex from Enterococcus hirae V-ATPase [bA3B3]


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3VR4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529626% PEG 3350, 0.1M HEPES, 0.2M Sodium chloride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal Properties
Matthews coefficientSolvent content
2.5852.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 122.11α = 90
b = 124.13β = 90
c = 245.33γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU1.0000SPring-8BL41XU

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
13.470.9999.80.13810.67.2520245202473.428
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)
13.43.581000.4074.67.47506

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 REPLACEMENTTHROUGHOUT3VR43.470.994920849208265199.60.199970.199970.197870.23914RANDOM92.677
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]
-2.89-2.485.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.838
r_dihedral_angle_3_deg17.148
r_dihedral_angle_4_deg14.722
r_dihedral_angle_1_deg5.176
r_scangle_it1.046
r_angle_refined_deg1.032
r_scbond_it0.608
r_mcangle_it0.398
r_mcbond_it0.205
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.838
r_dihedral_angle_3_deg17.148
r_dihedral_angle_4_deg14.722
r_dihedral_angle_1_deg5.176
r_scangle_it1.046
r_angle_refined_deg1.032
r_scbond_it0.608
r_mcangle_it0.398
r_mcbond_it0.205
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_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 Atoms24131
Nucleic Acid Atoms
Solvent Atoms71
Heterogen Atoms64

Software

Software
Software NamePurpose
BSSdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling