6ECH

Pyruvate Kinase Isoform L-type with phosphorylated Ser12 (pS12) in complex with FBP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4IP7PDB entry 4IP7

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52910.1 M HEPES, pH 7.5, 10% ethylene glycol, 8-12% PEG8000
Crystal Properties
Matthews coefficientSolvent content
2.9357.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.55α = 90
b = 108.9β = 90
c = 296.84γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2018-06-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.9795CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1949.521000.0850.0920.0350.99814.56.7144911
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.192.2399.80.8890.9640.3720.8146.6

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 REPLACEMENTTHROUGHOUTPDB entry 4IP72.1949.52137771712499.940.18370.1810.2379RANDOM45.771
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]
1.611.06-2.67
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.527
r_dihedral_angle_4_deg17.984
r_dihedral_angle_3_deg16.229
r_dihedral_angle_1_deg6.752
r_angle_refined_deg1.464
r_angle_other_deg0.919
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.527
r_dihedral_angle_4_deg17.984
r_dihedral_angle_3_deg16.229
r_dihedral_angle_1_deg6.752
r_angle_refined_deg1.464
r_angle_other_deg0.919
r_chiral_restr0.067
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms16061
Nucleic Acid Atoms
Solvent Atoms1201
Heterogen Atoms380

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction