1U5A

Plasmodium falciparum lactate dehydrogenase complexed with 3,5-dihydroxy-2-naphthoic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LDGPDb entry 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
2.3948.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.206α = 90
b = 85.263β = 90
c = 91.828γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEMirrors2001-08-24MSINGLE 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
11.83098.60.059163296462920822
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)
11.81.9496.80.243.735651

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 REPLACEMENTTHROUGHOUTPDb entry 1LDG1.829.242867127210146196.950.146740.146740.145330.17309RANDOM13.749
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]
-0.71.15-0.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.267
r_scangle_it3.663
r_scbond_it2.259
r_angle_refined_deg1.424
r_mcangle_it1.331
r_angle_other_deg1.089
r_mcbond_it0.748
r_nbd_refined0.322
r_symmetry_vdw_other0.287
r_nbd_other0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.267
r_scangle_it3.663
r_scbond_it2.259
r_angle_refined_deg1.424
r_mcangle_it1.331
r_angle_other_deg1.089
r_mcbond_it0.748
r_nbd_refined0.322
r_symmetry_vdw_other0.287
r_nbd_other0.238
r_xyhbond_nbd_refined0.136
r_symmetry_hbond_refined0.136
r_symmetry_vdw_refined0.126
r_nbtor_other0.085
r_chiral_restr0.081
r_bond_refined_d0.014
r_gen_planes_other0.009
r_gen_planes_refined0.008
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2314
Nucleic Acid Atoms
Solvent Atoms268
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing