6YI9

Crystal structure of the rat cytosolic PCK1, acetylated on Lys244


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QF2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3350 magnesium formate HEPES pH 8 NaF
Crystal Properties
Matthews coefficientSolvent content
2.2144.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.384α = 90
b = 85.225β = 90
c = 119.669γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.752087.30.0910.99713.25.755039
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.840.874

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 REPLACEMENTTHROUGHOUT2QF21.7519.9552817216787.210.172010.170370.21151RANDOM23.795
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]
-1.011.87-0.85
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.529
r_dihedral_angle_4_deg18.868
r_dihedral_angle_3_deg15.545
r_long_range_B_refined8.737
r_long_range_B_other8.731
r_dihedral_angle_1_deg7.332
r_scangle_other4.33
r_mcangle_it2.855
r_mcangle_other2.855
r_scbond_it2.802
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg29.529
r_dihedral_angle_4_deg18.868
r_dihedral_angle_3_deg15.545
r_long_range_B_refined8.737
r_long_range_B_other8.731
r_dihedral_angle_1_deg7.332
r_scangle_other4.33
r_mcangle_it2.855
r_mcangle_other2.855
r_scbond_it2.802
r_scbond_other2.802
r_mcbond_it1.896
r_mcbond_other1.896
r_angle_refined_deg1.575
r_angle_other_deg0.548
r_chiral_restr0.072
r_bond_refined_d0.012
r_gen_planes_refined0.009
r_bond_other_d0.001
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 Atoms4872
Nucleic Acid Atoms
Solvent Atoms435
Heterogen Atoms80

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing