3L6O

Crystal Structure of Phosphate bound apo Glyceraldehyde-3-phosphate dehydrogenase 1 from MRSA252 at 2.2 Angstrom resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.72980.1M Tris-HCl pH 8.7, 32% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
1.8433.15

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.955α = 90
b = 93.683β = 106.84
c = 89.054γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++Varimax mirrors2009-12-09MSINGLE 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
12.233.3499.70.0886.83.615334836.1
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)
12.22.2897.30.4282.33.335203

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 REPLACEMENTTHROUGHOUT3H482.22053279270699.670.2180.2160.258RANDOM63.605
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]
0.78-0.321.08-2.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.555
r_dihedral_angle_4_deg23.672
r_dihedral_angle_3_deg16.015
r_dihedral_angle_1_deg6.688
r_scangle_it6.588
r_scbond_it3.929
r_mcangle_it1.507
r_angle_refined_deg1.469
r_mcbond_it0.774
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.555
r_dihedral_angle_4_deg23.672
r_dihedral_angle_3_deg16.015
r_dihedral_angle_1_deg6.688
r_scangle_it6.588
r_scbond_it3.929
r_mcangle_it1.507
r_angle_refined_deg1.469
r_mcbond_it0.774
r_chiral_restr0.095
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10116
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms20

Software

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