4O59

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, 0.15 M malic acid pH 7.0, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.5752.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.703α = 90
b = 125.273β = 118.02
c = 83.602γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-04-12MSINGLE 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
11.525098.50.0943.1220468-3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1J0X1.5247.8-32062131088698.30.179770.178220.20904RANDOM17.959
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]
0.470.58-0.22-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.956
r_dihedral_angle_4_deg23.088
r_dihedral_angle_3_deg13.315
r_dihedral_angle_1_deg6.696
r_long_range_B_refined5.034
r_long_range_B_other5.016
r_scangle_other4.241
r_scbond_it2.837
r_scbond_other2.837
r_mcangle_other2.187
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.956
r_dihedral_angle_4_deg23.088
r_dihedral_angle_3_deg13.315
r_dihedral_angle_1_deg6.696
r_long_range_B_refined5.034
r_long_range_B_other5.016
r_scangle_other4.241
r_scbond_it2.837
r_scbond_other2.837
r_mcangle_other2.187
r_mcangle_it2.185
r_angle_refined_deg2.062
r_mcbond_it1.604
r_mcbond_other1.596
r_angle_other_deg0.924
r_chiral_restr0.127
r_bond_refined_d0.02
r_gen_planes_refined0.012
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 Atoms582
Heterogen Atoms176

Software

Software
Software NamePurpose
Xtaldata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling