1U5C

Plasmodium falciparum lactate dehydrogenase complexed with 3,7-dihydroxynaphthalene-2-carboxylic acid and NAD+


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
2.3647.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.225α = 90
b = 86.017β = 90
c = 91.07γ = 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
12.63097.60.1277.1710105984822
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)
12.62.69990.2943.13992

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 1LDG2.6529.369013857244195.280.15790.15790.153740.23945RANDOM14.362
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]
-1.521.65-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.201
r_scangle_it2.941
r_scbond_it1.721
r_angle_refined_deg1.587
r_mcangle_it1.217
r_angle_other_deg0.793
r_mcbond_it0.653
r_nbd_refined0.312
r_symmetry_vdw_other0.277
r_nbd_other0.237
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.201
r_scangle_it2.941
r_scbond_it1.721
r_angle_refined_deg1.587
r_mcangle_it1.217
r_angle_other_deg0.793
r_mcbond_it0.653
r_nbd_refined0.312
r_symmetry_vdw_other0.277
r_nbd_other0.237
r_symmetry_hbond_refined0.22
r_xyhbond_nbd_refined0.186
r_symmetry_vdw_refined0.181
r_nbtor_other0.087
r_chiral_restr0.075
r_bond_refined_d0.017
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2305
Nucleic Acid Atoms
Solvent Atoms132
Heterogen Atoms59

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing