3AON | pdb_00003aon

Crystal structure of the central axis (NtpD-NtpG) in the catalytic portion of Enterococcus hirae V-type sodium ATPase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529318% PEG 3350, 0.2 M Sodium Nitrate, 0.1M MES-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.1943.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.787α = 90
b = 68.433β = 114.99
c = 51.153γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX225HE2009-07-17MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL41XU0.9791, 0.9794, 1.0000SPring-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
1234.1697.20.0910.76.1216982169829
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)
122.1196.30.5612.86.13128

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMADTHROUGHOUT231.982239821696108596.870.19740.19740.194450.2020.251610.2521RANDOM41.498
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]
-0.45-3.3-1.54-0.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.267
r_dihedral_angle_3_deg17.468
r_dihedral_angle_4_deg13.411
r_dihedral_angle_1_deg5.019
r_scangle_it3.399
r_scbond_it2.009
r_mcangle_it1.306
r_angle_refined_deg1.276
r_mcbond_it0.678
r_chiral_restr0.091
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2284
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms4

Software

Software
Software NamePurpose
BSSdata collection
SOLVEphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling