3KV3

Crystal structure of C151S mutant of Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH 1)from methicillin resistant Staphylococcus aureus MRSA252 complexed with NAD and G3P


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3H48 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22980.1 (M) Tris-HCl, pH 8.2, 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1442.46

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.519α = 90
b = 104.49β = 108.03
c = 91.192γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax mirrors2009-06-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
12.586.7198.80.0849.73.734175954.2
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)
12.52.5997.70.3443.23.714116

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 REPLACEMENTTHROUGHOUT3H482.521.3541750210098.560.190.1870.238RANDOM39.086
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]
-0.85-0.442.53-1.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.865
r_dihedral_angle_4_deg25.182
r_dihedral_angle_3_deg15.761
r_dihedral_angle_1_deg6.562
r_scangle_it6.425
r_scbond_it3.809
r_angle_refined_deg1.571
r_mcangle_it1.416
r_mcbond_it0.661
r_chiral_restr0.094
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.865
r_dihedral_angle_4_deg25.182
r_dihedral_angle_3_deg15.761
r_dihedral_angle_1_deg6.562
r_scangle_it6.425
r_scbond_it3.809
r_angle_refined_deg1.571
r_mcangle_it1.416
r_mcbond_it0.661
r_chiral_restr0.094
r_bond_refined_d0.015
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10124
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms220

Software

Software
Software NamePurpose
d*TREKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
d*TREKdata reduction