1T24

Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LDG 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291MPD, Hepes, Imidazole, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.240

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.488α = 90
b = 85.914β = 90
c = 90.447γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEmirrors2000-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

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
11.729.361000.058182.7349393344822
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)
11.71.761000.1885.1

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 REPLACEMENTTHROUGHOUT1LDG1.729.3633448314231677950.14370.14370.142470.16668RANDOM8.947
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]
-0.410.98-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.351
r_dihedral_angle_1_deg3.896
r_scangle_it3.517
r_scbond_it2.119
r_angle_refined_deg1.544
r_angle_other_deg1.206
r_mcangle_it1.136
r_mcbond_it0.586
r_symmetry_hbond_refined0.448
r_nbtor_other0.446
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.351
r_dihedral_angle_1_deg3.896
r_scangle_it3.517
r_scbond_it2.119
r_angle_refined_deg1.544
r_angle_other_deg1.206
r_mcangle_it1.136
r_mcbond_it0.586
r_symmetry_hbond_refined0.448
r_nbtor_other0.446
r_nbd_refined0.224
r_symmetry_vdw_refined0.213
r_nbd_other0.194
r_symmetry_vdw_other0.189
r_xyhbond_nbd_refined0.146
r_chiral_restr0.077
r_bond_refined_d0.011
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2383
Nucleic Acid Atoms
Solvent Atoms322
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing