2VGB

HUMAN ERYTHROCYTE PYRUVATE KINASE


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PKNPDB ENTRY 1PKN

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5295RECOMBINANT WILD-TYPE RPK WAS CRYSTALLIZED USING THE VAPOR DIFFUSION METHOD AT 22 C. WELL SOLUTIONS CONSISTED OF 50 MM MES/KOH, PH 6.4, 10 MM MNSO4, AND 10-14% W/V PEG8000. HANGING DROPS WERE FORMED BY MIXING EQUAL VOLUMES OF 12 MG/ML PROTEIN IN 50 MM KCL, 5 MM FBP, 5 MM PHOSPHOGLYCOLATE, 20 MM POTASSIUM PHOSPHATE, PH 7.0, AND WELL SOLUTIONS.
Crystal Properties
Matthews coefficientSolvent content
2.550.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.413α = 90
b = 172.058β = 92.46
c = 85.512γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRFESRFID14-2

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
12.72095.90.0813.42.155091
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)
12.72.786.50.242.42.1

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 1PKN2.732052174278096.30.2290.2270.271RANDOM40.86
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]
-0.140.120.2-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.011
r_dihedral_angle_4_deg23.116
r_dihedral_angle_3_deg20.809
r_dihedral_angle_1_deg5.423
r_scangle_it2.564
r_scbond_it1.546
r_angle_refined_deg1.513
r_mcangle_it0.785
r_symmetry_vdw_refined0.54
r_mcbond_it0.399
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.011
r_dihedral_angle_4_deg23.116
r_dihedral_angle_3_deg20.809
r_dihedral_angle_1_deg5.423
r_scangle_it2.564
r_scbond_it1.546
r_angle_refined_deg1.513
r_mcangle_it0.785
r_symmetry_vdw_refined0.54
r_mcbond_it0.399
r_nbtor_refined0.322
r_symmetry_hbond_refined0.315
r_nbd_refined0.257
r_xyhbond_nbd_refined0.163
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15423
Nucleic Acid Atoms
Solvent Atoms65
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing