2XE8

The complete reaction cycle of human phosphoglycerate kinase: The open ternary complex with 3PG and AMP-PNP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3C39PDB ENTRY 3C39

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1830% PEG4000, 100MM TRIS PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2545.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.32α = 90
b = 71.17β = 90
c = 91.47γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDGE 2212009-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.792098.60.0710.12.936815319.4
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)
11.791.8897.10.293.62.7

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 3C391.792034947183998.150.200380.198160.24252RANDOM21.853
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]
-0.07-0.190.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.394
r_dihedral_angle_4_deg22.258
r_dihedral_angle_3_deg15.634
r_dihedral_angle_1_deg6.866
r_scangle_it5.228
r_scbond_it3.434
r_angle_refined_deg1.959
r_mcangle_it1.854
r_mcbond_it1.13
r_chiral_restr0.141
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.394
r_dihedral_angle_4_deg22.258
r_dihedral_angle_3_deg15.634
r_dihedral_angle_1_deg6.866
r_scangle_it5.228
r_scbond_it3.434
r_angle_refined_deg1.959
r_mcangle_it1.854
r_mcbond_it1.13
r_chiral_restr0.141
r_bond_refined_d0.023
r_gen_planes_refined0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms3096
Nucleic Acid Atoms
Solvent Atoms140
Heterogen Atoms42

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing