2VFH

Crystal structure of the F96W mutant of Plasmodium falciparum triosephosphate isomerase complexed with 3-phosphoglycerate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O5XPDB ENTRY 1O5X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
150.1 M SODIUM ACETATE, PH 4.0-5.5, PEG 1450 8-24%
Crystal Properties
Matthews coefficientSolvent content
2.143.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.543α = 90
b = 51.182β = 92.4
c = 86.568γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHOSMIC MIRROR2007-02-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
125099.60.0813.5331777
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)
122.0798.70.422.42.7

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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 1O5X244.0730156160499.510.196040.193390.2448RANDOM24.718
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]
-0.02-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.911
r_dihedral_angle_3_deg14.609
r_dihedral_angle_4_deg12.422
r_dihedral_angle_1_deg5.642
r_scangle_it1.743
r_angle_refined_deg1.092
r_scbond_it1.085
r_mcangle_it0.712
r_mcbond_it0.398
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.911
r_dihedral_angle_3_deg14.609
r_dihedral_angle_4_deg12.422
r_dihedral_angle_1_deg5.642
r_scangle_it1.743
r_angle_refined_deg1.092
r_scbond_it1.085
r_mcangle_it0.712
r_mcbond_it0.398
r_nbtor_refined0.296
r_nbd_refined0.181
r_symmetry_vdw_refined0.179
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.115
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3925
Nucleic Acid Atoms
Solvent Atoms440
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing