4YPL

Crystal structure of a hexameric LonA protease bound to three ADPs


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4YPN4YPN, 1QZM and 1RR9
experimental modelPDB 1QZM4YPN, 1QZM and 1RR9
experimental modelPDB 1RR94YPN, 1QZM and 1RR9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.72950.1 M Tris-HCl pH 8.7, 0.1 M CaCl2, 10-13% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.6353.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 169.044α = 90
b = 169.128β = 90
c = 135.361γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray200CCDRAYONIX MX300HE2014-11-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL44XU0.9SPring-8BL44XU

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
13.455099.50.1685.652050459682
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.453.4799.62.535.4

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 REPLACEMENTTHROUGHOUT4YPN, 1QZM and 1RR93.453045968244793.470.238590.23720.2648RANDOM66.574
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]
-1.3810.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.025
r_dihedral_angle_3_deg22.447
r_dihedral_angle_4_deg19.299
r_dihedral_angle_1_deg7.984
r_long_range_B_refined7.788
r_long_range_B_other7.788
r_mcangle_it4.656
r_mcangle_other4.656
r_scangle_other4.025
r_angle_other_deg3.543
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.025
r_dihedral_angle_3_deg22.447
r_dihedral_angle_4_deg19.299
r_dihedral_angle_1_deg7.984
r_long_range_B_refined7.788
r_long_range_B_other7.788
r_mcangle_it4.656
r_mcangle_other4.656
r_scangle_other4.025
r_angle_other_deg3.543
r_mcbond_it2.737
r_mcbond_other2.737
r_scbond_it2.244
r_scbond_other2.244
r_angle_refined_deg1.517
r_chiral_restr0.075
r_bond_refined_d0.008
r_gen_planes_refined0.008
r_gen_planes_other0.004
r_bond_other_d
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 Atoms25091
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms267

Software

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