4AXX

The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP 3-phosphoglycerate and beryllium trifluoride


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.532% PEG2000MME, 0.1M BIS/TRIS PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.130.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.82α = 90
b = 90.8β = 90
c = 108.54γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRROR2009-04-08MSINGLE 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
11.7429.586.90.0711.93.5346802
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)
11.741.8389.90.572.33.2

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 2WZC1.742032916173085.990.171610.169760.2065RANDOM18.934
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]
0.590.73-1.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.146
r_dihedral_angle_4_deg16.544
r_dihedral_angle_3_deg14.039
r_dihedral_angle_1_deg6.576
r_angle_refined_deg1.544
r_angle_other_deg0.907
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.146
r_dihedral_angle_4_deg16.544
r_dihedral_angle_3_deg14.039
r_dihedral_angle_1_deg6.576
r_angle_refined_deg1.544
r_angle_other_deg0.907
r_chiral_restr0.086
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.002
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_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 Atoms3055
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing