3LC1

Crystal Structure of H178N mutant of Glyceraldehyde-3-phosphate-dehydrogenase 1 (GAPDH 1) from Staphylococcus aureus MRSA252 complexed with NAD at 2.0 angstrom resolution.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.22770.1M Tris-HCl, pH 8.2, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.1843.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.849α = 90
b = 105.945β = 108.343
c = 91.473γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax mirrors2009-05-05MSINGLE 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
1286.8295.30.0649.93.738007130.5
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)
122.0792.40.3752.53.637739

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 REPLACEMENTTHROUGHOUT3H48229.0680066400395.240.1990.1970.242RANDOM32.455
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]
2.55-0.92-1.89-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.569
r_dihedral_angle_4_deg21.547
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg5.975
r_scangle_it2.452
r_scbond_it1.538
r_angle_refined_deg1.325
r_mcangle_it0.915
r_mcbond_it0.497
r_chiral_restr0.082
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.569
r_dihedral_angle_4_deg21.547
r_dihedral_angle_3_deg14.235
r_dihedral_angle_1_deg5.975
r_scangle_it2.452
r_scbond_it1.538
r_angle_refined_deg1.325
r_mcangle_it0.915
r_mcbond_it0.497
r_chiral_restr0.082
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10142
Nucleic Acid Atoms
Solvent Atoms413
Heterogen Atoms182

Software

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