1T2E

Plasmodium falciparum lactate dehydrogenase S245A, A327P mutant complexed with NADH and oxamate


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
2.140

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.066α = 90
b = 85.336β = 90
c = 89.714γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.11.488SRSPX14.1

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
11.852098.80.05921.34.9262932593422
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)
11.851.9396.20.2893.73153

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 REPLACEMENTTHROUGHOUT1LDG1.85202472623475125194.020.157610.157610.15580.19076RANDOM17.181
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]
-1.061.28-0.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.33
r_scangle_it5.473
r_dihedral_angle_1_deg4.249
r_scbond_it3.371
r_angle_refined_deg2.375
r_mcangle_it1.938
r_mcbond_it1.157
r_symmetry_hbond_refined0.942
r_nbd_refined0.358
r_symmetry_vdw_refined0.287
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg14.33
r_scangle_it5.473
r_dihedral_angle_1_deg4.249
r_scbond_it3.371
r_angle_refined_deg2.375
r_mcangle_it1.938
r_mcbond_it1.157
r_symmetry_hbond_refined0.942
r_nbd_refined0.358
r_symmetry_vdw_refined0.287
r_chiral_restr0.174
r_xyhbond_nbd_refined0.159
r_bond_refined_d0.023
r_gen_planes_refined0.011
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2404
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing