1T2D

Plasmodium falciparum lactate dehydrogenase complexed with NAD+ and oxalate


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 = 80.507α = 90
b = 86.583β = 90
c = 90.339γ = 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
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.9091EMBL/DESY, HAMBURGX11

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
11.13099.70.07222.55.612755012717722
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)
11.11.1295.60.4732.16036

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 REPLACEMENTTHROUGHOUT1LDG1.129.49122251116082616995.90.143240.143240.142790.15169RANDOM6.56
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.238
r_scangle_it2.225
r_sphericity_free1.61
r_scbond_it1.384
r_angle_other_deg1.305
r_angle_refined_deg1.287
r_sphericity_bonded1.043
r_mcangle_it0.982
r_rigid_bond_restr0.655
r_mcbond_it0.559
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.238
r_scangle_it2.225
r_sphericity_free1.61
r_scbond_it1.384
r_angle_other_deg1.305
r_angle_refined_deg1.287
r_sphericity_bonded1.043
r_mcangle_it0.982
r_rigid_bond_restr0.655
r_mcbond_it0.559
r_symmetry_vdw_other0.314
r_nbd_other0.238
r_symmetry_vdw_refined0.23
r_nbd_refined0.214
r_symmetry_hbond_refined0.107
r_chiral_restr0.105
r_xyhbond_nbd_refined0.087
r_nbtor_other0.084
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2383
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms56

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing