1U4S

Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedisulphonic acid


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LDGPDB model 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
2.448.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.094α = 90
b = 86.096β = 90
c = 91.327γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCEMirrors2001-09-14MSINGLE 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
123090.90.05513.66198661986622
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)
122.1579.50.1744.123421

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 model 1LDG229.362036019321103994.250.138430.138430.135780.18767RANDOM16.842
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]
-1.61.73-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.685
r_scangle_it3.76
r_scbond_it2.325
r_angle_refined_deg1.481
r_mcangle_it1.336
r_angle_other_deg0.829
r_mcbond_it0.77
r_nbd_refined0.316
r_symmetry_vdw_other0.291
r_nbd_other0.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.685
r_scangle_it3.76
r_scbond_it2.325
r_angle_refined_deg1.481
r_mcangle_it1.336
r_angle_other_deg0.829
r_mcbond_it0.77
r_nbd_refined0.316
r_symmetry_vdw_other0.291
r_nbd_other0.24
r_symmetry_vdw_refined0.171
r_xyhbond_nbd_refined0.143
r_symmetry_hbond_refined0.127
r_chiral_restr0.088
r_nbtor_other0.084
r_bond_refined_d0.016
r_gen_planes_refined0.007
r_gen_planes_other0.007
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2322
Nucleic Acid Atoms
Solvent Atoms235
Heterogen Atoms18

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing