4O63

Co-enzyme Induced Conformational Changes in Bovine Eye Glyceraldehyde 3-Phosphate Dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J0X 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION727720% PEG3350 and 0.2M succinate, pH 7.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5852.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.752α = 90
b = 126.205β = 118.13
c = 83.228γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 24-ID-C0.97918APS24-ID-C

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
11.935099.30.0884.1108672-3

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 REPLACEMENTTHROUGHOUT1J0X1.9346.86101816536897.990.190040.187790.23352RANDOM26.295
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]
-1.150.280.640.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.039
r_dihedral_angle_4_deg23.16
r_dihedral_angle_3_deg14.665
r_dihedral_angle_1_deg6.748
r_long_range_B_refined5.285
r_long_range_B_other5.278
r_scangle_other4.403
r_scbond_it2.946
r_scbond_other2.942
r_mcangle_it2.935
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.039
r_dihedral_angle_4_deg23.16
r_dihedral_angle_3_deg14.665
r_dihedral_angle_1_deg6.748
r_long_range_B_refined5.285
r_long_range_B_other5.278
r_scangle_other4.403
r_scbond_it2.946
r_scbond_other2.942
r_mcangle_it2.935
r_mcangle_other2.935
r_mcbond_it2.207
r_mcbond_other2.206
r_angle_refined_deg1.905
r_angle_other_deg0.881
r_chiral_restr0.117
r_bond_refined_d0.018
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10052
Nucleic Acid Atoms
Solvent Atoms304
Heterogen Atoms132

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling