4YPN

Crystal structure of a LonA fragment containing the 3-helix bundle and the AAA-alpha/beta domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M6A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.52950.1 M sodium citrate pH 5.5, 25 % PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9637.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.203α = 90
b = 63.892β = 90
c = 69.298γ = 90
Symmetry
Space GroupP 21 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200PIXELDECTRIS PILATUS 2M-F2013-01-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-1A1.1Photon FactoryBL-1A

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
12.075099.80.08619.496.116502156282
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)
12.072.141000.5754.626.2

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3M6A2.07301562783399.190.187470.184880.23657RANDOM37.758
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]
0.39-0.420.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.413
r_dihedral_angle_4_deg22.701
r_dihedral_angle_3_deg15.627
r_long_range_B_refined8.089
r_long_range_B_other8.022
r_dihedral_angle_1_deg6.981
r_scangle_other5.591
r_mcangle_it4.15
r_mcangle_other4.149
r_scbond_it3.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.413
r_dihedral_angle_4_deg22.701
r_dihedral_angle_3_deg15.627
r_long_range_B_refined8.089
r_long_range_B_other8.022
r_dihedral_angle_1_deg6.981
r_scangle_other5.591
r_mcangle_it4.15
r_mcangle_other4.149
r_scbond_it3.56
r_scbond_other3.559
r_mcbond_it2.764
r_mcbond_other2.751
r_angle_refined_deg1.892
r_angle_other_deg0.947
r_chiral_restr0.132
r_bond_refined_d0.018
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1985
Nucleic Acid Atoms
Solvent Atoms85
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data processing
HKL-2000data scaling