7C5H

Crystal Structure of Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli at 2.09 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1293100mM sodium PBS pH 6.1, 16%(w/v) PEG 1000, 200mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2745.73

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.778α = 90
b = 89.778β = 90
c = 340.953γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL18U10.97776SSRFBL18U1

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
12.095099.70.15413.281383301
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)
12.092.1399.30.6043.1412.1

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 REPLACEMENTTHROUGHOUT7C5F2.094079044418199.610.153360.150740.20274RANDOM21.843
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]
0.440.44-0.88
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.899
r_dihedral_angle_4_deg21.575
r_dihedral_angle_3_deg13.311
r_dihedral_angle_1_deg7.287
r_long_range_B_refined5.929
r_long_range_B_other5.919
r_scangle_other4.289
r_scbond_it2.799
r_scbond_other2.797
r_mcangle_it2.517
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.899
r_dihedral_angle_4_deg21.575
r_dihedral_angle_3_deg13.311
r_dihedral_angle_1_deg7.287
r_long_range_B_refined5.929
r_long_range_B_other5.919
r_scangle_other4.289
r_scbond_it2.799
r_scbond_other2.797
r_mcangle_it2.517
r_mcangle_other2.517
r_angle_refined_deg1.937
r_mcbond_it1.73
r_mcbond_other1.728
r_angle_other_deg1.028
r_chiral_restr0.106
r_bond_refined_d0.018
r_gen_planes_refined0.009
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 Atoms10060
Nucleic Acid Atoms
Solvent Atoms881
Heterogen Atoms265

Software

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