7C5L

Crystal Structure of C150S mutant of Glyceraldehyde-3-phosphate-dehydrogenase1 from Escherichia coli at 2.1 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5293100mM sodium acetate pH4.5, 30% (w/v) PEG 400, 200mM Ca(OAC)2
Crystal Properties
Matthews coefficientSolvent content
2.3748.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.4α = 90
b = 89.4β = 90
c = 340.266γ = 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
12.09501000.17419.6719.482932
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)
12.12.141000.5494.3

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 REPLACEMENTTHROUGHOUT7C5F2.0947.88878398414899.640.150960.148320.20074RANDOM23.654
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]
0.510.51-1.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.072
r_dihedral_angle_4_deg19.236
r_dihedral_angle_3_deg13.094
r_dihedral_angle_1_deg7.077
r_long_range_B_refined5.884
r_long_range_B_other5.873
r_scangle_other4.306
r_scbond_it2.884
r_scbond_other2.884
r_mcangle_it2.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.072
r_dihedral_angle_4_deg19.236
r_dihedral_angle_3_deg13.094
r_dihedral_angle_1_deg7.077
r_long_range_B_refined5.884
r_long_range_B_other5.873
r_scangle_other4.306
r_scbond_it2.884
r_scbond_other2.884
r_mcangle_it2.75
r_mcangle_other2.75
r_mcbond_it1.98
r_mcbond_other1.973
r_angle_refined_deg1.889
r_angle_other_deg1.029
r_chiral_restr0.109
r_bond_refined_d0.017
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10077
Nucleic Acid Atoms
Solvent Atoms988
Heterogen Atoms190

Software

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