2ZGV

Crystal Structure of human phosphoglycerate kinase bound to D-ADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1VJC 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.32912.6M NaKPO4, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1442.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.956α = 90
b = 106.627β = 97.3
c = 50.35γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100AREA DETECTOR2007-05-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.934ESRFID14-4

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
1245.220.690.04811.32.6169871698719.2
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
22.110.310.3232.921136

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 REPLACEMENTTHROUGHOUT1VJC245.221698746668.740.177820.175570.25828RANDOM19.739
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]
0.120.61-0.580.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.472
r_dihedral_angle_4_deg19.349
r_dihedral_angle_3_deg17.235
r_dihedral_angle_1_deg6.619
r_scangle_it4.43
r_scbond_it2.696
r_angle_refined_deg1.697
r_mcangle_it1.542
r_mcbond_it0.863
r_chiral_restr0.109
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.472
r_dihedral_angle_4_deg19.349
r_dihedral_angle_3_deg17.235
r_dihedral_angle_1_deg6.619
r_scangle_it4.43
r_scbond_it2.696
r_angle_refined_deg1.697
r_mcangle_it1.542
r_mcbond_it0.863
r_chiral_restr0.109
r_bond_refined_d0.017
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3024
Nucleic Acid Atoms
Solvent Atoms234
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing