1T25

Plasmodium falciparum lactate dehydrogenase complexed with NADH and 3-hydroxyisoxazole-4-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
2.340

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.241α = 90
b = 87.185β = 90
c = 92.094γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42002-01-01MSINGLE 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
11.929.7599.80.06619.54.1260932411922
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)
11.91.991000.2274.7

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 REPLACEMENTTHROUGHOUT1LDG1.929.752609324119129097.210.153510.153510.151790.18576RANDOM12.609
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]
-1.111.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.151
r_dihedral_angle_1_deg4.037
r_scangle_it3.879
r_scbond_it2.352
r_angle_refined_deg1.667
r_mcangle_it1.437
r_angle_other_deg1.236
r_symmetry_hbond_refined1.156
r_mcbond_it0.782
r_nbtor_other0.631
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.151
r_dihedral_angle_1_deg4.037
r_scangle_it3.879
r_scbond_it2.352
r_angle_refined_deg1.667
r_mcangle_it1.437
r_angle_other_deg1.236
r_symmetry_hbond_refined1.156
r_mcbond_it0.782
r_nbtor_other0.631
r_nbd_refined0.216
r_nbd_other0.187
r_symmetry_vdw_other0.185
r_symmetry_vdw_refined0.137
r_xyhbond_nbd_refined0.129
r_chiral_restr0.09
r_xyhbond_nbd_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.006
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 Atoms233
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing