1U4O

Plasmodium falciparum lactate dehydrogenase complexed with 2,6-naphthalenedicarboxylic 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
2.346.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.196α = 90
b = 85.225β = 90
c = 92.232γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAC Science DIP-2020Mirrors2001-09-03MSINGLE 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
11.730960.08713.573379422
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)
11.71.7893.20.293.33

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 1LDG1.729.243327431601167394.570.146890.146890.145140.18054RANDOM11.329
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]
-0.441.03-0.59
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.555
r_scangle_it3.137
r_scbond_it1.969
r_angle_refined_deg1.39
r_angle_other_deg1.354
r_mcangle_it1.145
r_mcbond_it0.654
r_nbd_refined0.321
r_symmetry_vdw_other0.268
r_nbd_other0.235
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.555
r_scangle_it3.137
r_scbond_it1.969
r_angle_refined_deg1.39
r_angle_other_deg1.354
r_mcangle_it1.145
r_mcbond_it0.654
r_nbd_refined0.321
r_symmetry_vdw_other0.268
r_nbd_other0.235
r_symmetry_hbond_refined0.181
r_symmetry_vdw_refined0.169
r_xyhbond_nbd_refined0.15
r_chiral_restr0.112
r_nbtor_other0.085
r_bond_refined_d0.013
r_gen_planes_other0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2342
Nucleic Acid Atoms
Solvent Atoms319
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing