2WZB

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP, 3PG and magnesium trifluoride


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.522% PEG2000MME, 0.1M BIS/TRIS PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.2250

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.43α = 90
b = 92.18β = 90
c = 109γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDGE2112009-01-23MSINGLE 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
11.472099.10.0513.33.668247313.6
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)
11.471.55980.323.33.5

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 3C391.472064731345298.760.162220.160940.1863RANDOM5.78
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]
0.64-0.65
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.078
r_dihedral_angle_4_deg16.678
r_dihedral_angle_3_deg12.335
r_dihedral_angle_1_deg9.022
r_scangle_it3.093
r_scbond_it1.98
r_angle_refined_deg1.779
r_mcangle_it1.121
r_angle_other_deg0.936
r_mcbond_it0.655
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.078
r_dihedral_angle_4_deg16.678
r_dihedral_angle_3_deg12.335
r_dihedral_angle_1_deg9.022
r_scangle_it3.093
r_scbond_it1.98
r_angle_refined_deg1.779
r_mcangle_it1.121
r_angle_other_deg0.936
r_mcbond_it0.655
r_mcbond_other0.198
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.002
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_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 Atoms3040
Nucleic Acid Atoms
Solvent Atoms617
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing