3L4S

Crystal structure of C151G mutant of Glyceraldehyde 3-phosphate dehydrogenase 1 (GAPDH1) 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 DROP8.52980.1 (M) Tris-HCl, pH8.5, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.0840.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.593α = 90
b = 102.936β = 109.31
c = 90.652γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax mirrors2009-10-10MSINGLE 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
12.285.5594.90.0838.33.636008457048534.3
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)
12.22.2898.60.42.53.475916

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3H482.227.766008457048303599.550.199610.197070.24877RANDOM45.522
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]
-1.61-0.813.19-2.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.467
r_dihedral_angle_4_deg21.76
r_dihedral_angle_3_deg15.727
r_scangle_it6.974
r_dihedral_angle_1_deg6.876
r_scbond_it4.219
r_angle_refined_deg1.699
r_mcangle_it1.443
r_mcbond_it0.694
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.467
r_dihedral_angle_4_deg21.76
r_dihedral_angle_3_deg15.727
r_scangle_it6.974
r_dihedral_angle_1_deg6.876
r_scbond_it4.219
r_angle_refined_deg1.699
r_mcangle_it1.443
r_mcbond_it0.694
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10106
Nucleic Acid Atoms
Solvent Atoms263
Heterogen Atoms220

Software

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