6K31

Crystal structure of pyrophosphate-dependent phosphoenolpyruvate carboxykinase (PPi-PEPCK)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293HEPES, PEG 400, magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
2.9357.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 160.439α = 90
b = 160.439β = 90
c = 200.16γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95PIXELDECTRIS PILATUS3 6M2016-11-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A0.97887Photon FactoryBL-17A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
12.648.121000.0490.99919.220.191847
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.62.640.3890.837

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.648.1287201459599.970.198030.195760.2414RANDOM54.565
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]
-24.11-24.1148.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.501
r_dihedral_angle_4_deg17.773
r_dihedral_angle_3_deg17
r_long_range_B_refined9.974
r_long_range_B_other9.971
r_scangle_other7.384
r_dihedral_angle_1_deg7.014
r_mcangle_other6.813
r_mcangle_it6.812
r_scbond_it4.863
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.501
r_dihedral_angle_4_deg17.773
r_dihedral_angle_3_deg17
r_long_range_B_refined9.974
r_long_range_B_other9.971
r_scangle_other7.384
r_dihedral_angle_1_deg7.014
r_mcangle_other6.813
r_mcangle_it6.812
r_scbond_it4.863
r_scbond_other4.863
r_mcbond_it4.615
r_mcbond_other4.612
r_angle_refined_deg1.756
r_angle_other_deg1.323
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.009
r_bond_other_d0.006
r_gen_planes_other0.005
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 Atoms17120
Nucleic Acid Atoms
Solvent Atoms355
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing