7C5P

Crystal Structure Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli complexed with G3P at 2.35 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
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.339α = 90
b = 90.339β = 90
c = 341.547γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2016-09-19MSINGLE 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
12.3550.011000.191411.360156
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)
12.352.391000.6243.7

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 REPLACEMENTTHROUGHOUT7C5F2.355056884300399.460.157780.154970.20975RANDOM32.346
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]
1.081.08-2.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.169
r_dihedral_angle_4_deg20.005
r_dihedral_angle_3_deg13.678
r_dihedral_angle_1_deg7.227
r_long_range_B_refined6.034
r_long_range_B_other6.033
r_scangle_other4.474
r_mcangle_other3.343
r_mcangle_it3.341
r_scbond_it3.046
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.169
r_dihedral_angle_4_deg20.005
r_dihedral_angle_3_deg13.678
r_dihedral_angle_1_deg7.227
r_long_range_B_refined6.034
r_long_range_B_other6.033
r_scangle_other4.474
r_mcangle_other3.343
r_mcangle_it3.341
r_scbond_it3.046
r_scbond_other3.041
r_mcbond_it2.245
r_mcbond_other2.238
r_angle_refined_deg1.793
r_angle_other_deg1.012
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.008
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 Atoms10083
Nucleic Acid Atoms
Solvent Atoms615
Heterogen Atoms246

Software

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