3LC7

Crystal Structure of apo Glyceraldehyde-3-phosphate dehydrogenase 1 (GAPDH1) from methicllin 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 Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.288α = 90
b = 94.937β = 105.73
c = 86.552γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax mirrors2009-12-19MSINGLE 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 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
12.49483.31199.30.06119.13.7347463474638
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)
12.492.6396.70.2814.53.54921

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 REPLACEMENTTHROUGHOUT3H482.520346213462135499.890.1880.1870.249RANDOM40.942
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]
1.66-0.62-1.03-0.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.496
r_dihedral_angle_4_deg25.01
r_dihedral_angle_3_deg17.319
r_dihedral_angle_1_deg7.012
r_scangle_it6.45
r_scbond_it3.808
r_angle_refined_deg1.576
r_mcangle_it1.441
r_mcbond_it0.717
r_chiral_restr0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.496
r_dihedral_angle_4_deg25.01
r_dihedral_angle_3_deg17.319
r_dihedral_angle_1_deg7.012
r_scangle_it6.45
r_scbond_it3.808
r_angle_refined_deg1.576
r_mcangle_it1.441
r_mcbond_it0.717
r_chiral_restr0.1
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10075
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms12

Software

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