3LVF

Crystal Structure of holo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicillin resistant Staphylococcus aureus MRSA252 at 1.7 Angstrom resolution


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.1M Tris-HCl, pH8.5, 20% (w/v)PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthew coefficientSolvent content
2.1342.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.18α = 90
b = 104.874β = 107.72
c = 91.191γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax mirrors2009-05-14MSINGLE 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)Rrim I (All)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
11.730.7894.50.0590.0598.73.5212658438.7
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)
1.71.7693.60.432.43.3612506

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 REPLACEMENTTHROUGHOUT1HDG1.720126514635894.480.190.1890.221RANDOM39.013
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]
0.37-0.020.48-0.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.576
r_dihedral_angle_4_deg18.274
r_dihedral_angle_3_deg11.685
r_dihedral_angle_1_deg5.406
r_scangle_it3.23
r_scbond_it1.844
r_angle_refined_deg1.04
r_mcangle_it0.658
r_mcbond_it0.317
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.576
r_dihedral_angle_4_deg18.274
r_dihedral_angle_3_deg11.685
r_dihedral_angle_1_deg5.406
r_scangle_it3.23
r_scbond_it1.844
r_angle_refined_deg1.04
r_mcangle_it0.658
r_mcbond_it0.317
r_chiral_restr0.065
r_bond_refined_d0.006
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10152
Nucleic Acid Atoms
Solvent Atoms671
Heterogen Atoms176

Software

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