3OZG

Crystal Structure of Plasmodium falciparum Hypoxanthine-Guanine-Xanthine Phosphoribosyltransferase in complex with S-SerMe-ImmH phosphonate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CBJPDB ENTRY 1CBJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.4291200mM sodium citrate, 20% PEG3350, pH 7.4, vapor diffusion, sitting drop, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.2244.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 105.095α = 90
b = 110.628β = 90
c = 173.336γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A1.0809NSLSX29A

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
11.9932098.50.1495.97.367657
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)
11.9932.0788.70.7075.6

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1CBJ1.99319.9863967341797.710.221490.219170.26418RANDOM28.718
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]
0.03-0.160.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.717
r_dihedral_angle_4_deg20.061
r_dihedral_angle_3_deg16.985
r_dihedral_angle_1_deg6.171
r_scangle_it2.865
r_scbond_it1.841
r_angle_refined_deg1.503
r_mcangle_it1.098
r_mcbond_it0.575
r_chiral_restr0.102
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.717
r_dihedral_angle_4_deg20.061
r_dihedral_angle_3_deg16.985
r_dihedral_angle_1_deg6.171
r_scangle_it2.865
r_scbond_it1.841
r_angle_refined_deg1.503
r_mcangle_it1.098
r_mcbond_it0.575
r_chiral_restr0.102
r_bond_refined_d0.012
r_gen_planes_refined0.005
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 Atoms7354
Nucleic Acid Atoms
Solvent Atoms211
Heterogen Atoms124

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection