7C5R

Crystal Structure of C150S mutant Glyceraldehyde-3-phosphate dehydrogenase1 from Escherichia coli complexed with BPG at 2.31 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.2293100mM sodium PBS pH 6.2, 16%(w/v) PEG 1000, 200mM MgCl2
Crystal Properties
Matthews coefficientSolvent content
2.2545.27

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.398α = 90
b = 89.398β = 90
c = 340.821γ = 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
12.3150.011000.16613.511.461720
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)
12.312.351000.5353.33

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 REPLACEMENTTHROUGHOUT7C5F2.315058669307699.840.149420.146530.20332RANDOM28.778
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]
0.250.25-0.49
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.621
r_dihedral_angle_4_deg20.297
r_dihedral_angle_3_deg13.464
r_dihedral_angle_1_deg7.246
r_long_range_B_refined6.311
r_long_range_B_other6.299
r_scangle_other4.447
r_mcangle_it3.03
r_mcangle_other3.03
r_scbond_it2.913
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.621
r_dihedral_angle_4_deg20.297
r_dihedral_angle_3_deg13.464
r_dihedral_angle_1_deg7.246
r_long_range_B_refined6.311
r_long_range_B_other6.299
r_scangle_other4.447
r_mcangle_it3.03
r_mcangle_other3.03
r_scbond_it2.913
r_scbond_other2.913
r_mcbond_it2.035
r_mcbond_other2.035
r_angle_refined_deg1.826
r_angle_other_deg1.006
r_chiral_restr0.096
r_bond_refined_d0.018
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 Atoms10063
Nucleic Acid Atoms
Solvent Atoms894
Heterogen Atoms274

Software

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