7C5N

Crystal Structure of C150A+H177A mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli at 2.0 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.3293100mM sodium Cacodylate pH 6.3, 20%(w/v) PEG 1000, 200mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.3647.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.376α = 90
b = 89.376β = 90
c = 341.506γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2015-12-19MSINGLE 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
11.9950.011000.218.5519.596080
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)
11.992.021000.885.2518

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 REPLACEMENTTHROUGHOUT7C5F1.995090975474799.850.163910.161020.21896RANDOM26.921
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.611
r_dihedral_angle_4_deg17.974
r_dihedral_angle_3_deg12.786
r_dihedral_angle_1_deg6.906
r_long_range_B_refined6.338
r_long_range_B_other6.322
r_scangle_other4.886
r_scbond_it3.324
r_scbond_other3.324
r_mcangle_it2.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg42.611
r_dihedral_angle_4_deg17.974
r_dihedral_angle_3_deg12.786
r_dihedral_angle_1_deg6.906
r_long_range_B_refined6.338
r_long_range_B_other6.322
r_scangle_other4.886
r_scbond_it3.324
r_scbond_other3.324
r_mcangle_it2.89
r_mcangle_other2.89
r_mcbond_it2.197
r_mcbond_other2.196
r_angle_refined_deg1.937
r_angle_other_deg1.04
r_chiral_restr0.118
r_bond_refined_d0.019
r_gen_planes_refined0.01
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 Atoms10071
Nucleic Acid Atoms
Solvent Atoms1112
Heterogen Atoms196

Software

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