3LC2

Crystal Structure of Thioacyl-Glyceraldehyde-3-phosphate dehydrogenase 1(GAPDH 1) from methicillin resistant Staphylococcus aureus MRSA252


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52980.1M Tris-HCl pH 8.5, 32% (w/v) PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0941.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.057α = 90
b = 103.025β = 109.4
c = 90.303γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVarimax mirrors2009-12-19MSINGLE 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 Sym 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
12.79385.17899.20.1343.8294892948946
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)
12.792.9496.90.4972.73.74196

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 REPLACEMENTTHROUGHOUT3H482.82029373149299.820.1840.1810.241RANDOM37.376
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]
-0.98-1.332.33-2.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.147
r_dihedral_angle_4_deg20.644
r_dihedral_angle_3_deg17.302
r_scangle_it6.637
r_dihedral_angle_1_deg6.242
r_scbond_it3.722
r_angle_refined_deg1.432
r_mcangle_it1.31
r_mcbond_it0.626
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.147
r_dihedral_angle_4_deg20.644
r_dihedral_angle_3_deg17.302
r_scangle_it6.637
r_dihedral_angle_1_deg6.242
r_scbond_it3.722
r_angle_refined_deg1.432
r_mcangle_it1.31
r_mcbond_it0.626
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10124
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms61

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
XDSdata reduction
MOLREPphasing