9FDH | pdb_00009fdh

Closed Human phosphoglycerate kinase complex with BPG and ADP produced by cross-soaking a TSA crystal


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WZBstarting crystal complex

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5298Produced from MgF3 TSA crystals produced in 50 mM Tris (pH 7.5), 20 mM DTT, 25 mM MgCl2, 50 mM 3PG, and 10 mM ADP and supplemented with 20 mM NH4F and 1 mM deferoxamine. Cross-soaked with 35% PEG 2000 MME; 0.1 M Bis/Tris pH 6.5, 20 mM DTT, 25 mM MgCl2, 10mM ATP and 50 mM 3PG
Crystal Properties
Matthews coefficientSolvent content
2.1743.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.845α = 90
b = 91.626β = 90
c = 108.734γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray83PIXELDECTRIS EIGER2 XE 16M2016-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.97625DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)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
11.75670.1299.250.0290.0410.0290.99912.21.93932225.68
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.761.8299.30.3850.5440.3850.6872.21.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1.75670.0671.3639322200099.250.14960.14810.150.17770.1791
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d12.315
f_angle_d1.057
f_chiral_restr0.057
f_bond_d0.01
f_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3116
Nucleic Acid Atoms
Solvent Atoms246
Heterogen Atoms59

Software

Software
Software NamePurpose
PHENIXrefinement
xia2data scaling
xia2data reduction
PHENIXphasing