2B4T

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from Plasmodium falciparum at 2.25 Angstrom resolution reveals intriguing extra electron density in the active site


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J0Xpdb entry 1J0X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.529830% PEG 3350; 200 MILLIMOLAR NA F; 100 MILLIMOLAR BIS-TRIS-PROPANE, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.140.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.687α = 90
b = 106.056β = 107.24
c = 91.057γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315double crystal2005-03-04MSINGLE WAVELENGTH
21x-ray100CCDQUANTUM 315double crystal2005-03-04MSINGLE WAVELENGTH
1,21
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9807SSRLBL9-2
2SYNCHROTRONSSRL BEAMLINE BL9-20.9807SSRLBL9-2

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
1,22.546.625980.1017.93.54284342843-368.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,22.52.6497.80.4842.23.66197

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1J0X2.543.484067540675214797.690.175750.175750.173520.21677RANDOM48.808
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]
4.221.59-1.07-2.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_4_deg16.91
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg5.693
r_scangle_it2.797
r_scbond_it1.924
r_mcangle_it1.647
r_mcbond_it1.257
r_angle_refined_deg1.08
r_angle_other_deg0.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.973
r_dihedral_angle_4_deg16.91
r_dihedral_angle_3_deg13.659
r_dihedral_angle_1_deg5.693
r_scangle_it2.797
r_scbond_it1.924
r_mcangle_it1.647
r_mcbond_it1.257
r_angle_refined_deg1.08
r_angle_other_deg0.712
r_symmetry_hbond_refined0.283
r_mcbond_other0.249
r_symmetry_vdw_refined0.236
r_nbd_refined0.187
r_symmetry_vdw_other0.184
r_nbtor_refined0.173
r_nbd_other0.169
r_xyhbond_nbd_refined0.15
r_nbtor_other0.08
r_chiral_restr0.059
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10184
Nucleic Acid Atoms
Solvent Atoms232
Heterogen Atoms215

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing