7C7K

Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from Escherichia coli at 1.77 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7C5F 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.6293100 mM sodium PBS pH 6.6, 16%(w/v) PEG 1000, 200mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.4449.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.163α = 90
b = 90.163β = 90
c = 345.059γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2017-05-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.9776SSRFBL19U1

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
11.775099.80.10935.926.6139316
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)
11.771.898.90.6034.75

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 REPLACEMENTTHROUGHOUT7C5F1.7748.49132099678899.60.145030.143210.1808RANDOM23.786
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]
-0.06-0.060.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.602
r_dihedral_angle_4_deg20.537
r_dihedral_angle_3_deg11.959
r_dihedral_angle_1_deg6.917
r_long_range_B_refined6.566
r_long_range_B_other6.556
r_scangle_other5.353
r_scbond_it3.634
r_scbond_other3.634
r_mcangle_it2.607
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.602
r_dihedral_angle_4_deg20.537
r_dihedral_angle_3_deg11.959
r_dihedral_angle_1_deg6.917
r_long_range_B_refined6.566
r_long_range_B_other6.556
r_scangle_other5.353
r_scbond_it3.634
r_scbond_other3.634
r_mcangle_it2.607
r_mcangle_other2.607
r_angle_refined_deg2.111
r_mcbond_it1.985
r_mcbond_other1.983
r_angle_other_deg1.096
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10106
Nucleic Acid Atoms
Solvent Atoms1213
Heterogen Atoms178

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing