2Y3I

The structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA aluminium tetrafluoride


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WZCPDB ENTRY 2WZC

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.526% PEG 2000MME, 0.1 M BIS/TRIS PH 6.5 .
Crystal Properties
Matthews coefficientSolvent content
2.2946.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.419α = 90
b = 103.877β = 90
c = 203.094γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHKB2010-09-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-2ESRFID23-2

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
12.946.2490.70.137.7317028360
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)
12.93.0699.10.512.33.1

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 2WZC2.9201608784089.910.26470.262660.30322RANDOM31.534
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]
-0.53-3.123.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.748
r_dihedral_angle_3_deg23.306
r_dihedral_angle_4_deg22.525
r_dihedral_angle_1_deg5.783
r_angle_refined_deg1.683
r_angle_other_deg1.375
r_chiral_restr0.105
r_bond_other_d0.019
r_bond_refined_d0.017
r_gen_planes_refined0.008
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.748
r_dihedral_angle_3_deg23.306
r_dihedral_angle_4_deg22.525
r_dihedral_angle_1_deg5.783
r_angle_refined_deg1.683
r_angle_other_deg1.375
r_chiral_restr0.105
r_bond_other_d0.019
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_gen_planes_other0.002
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
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 Atoms6204
Nucleic Acid Atoms
Solvent Atoms16
Heterogen Atoms90

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing