1T2C

Plasmodium falciparum lactate dehydrogenase complexed with NADH


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 = 81.136α = 90
b = 87.124β = 90
c = 92.212γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42001-01-01MSINGLE 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
123098.30.04428.54219122152122
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)
122.0999.80.10510.12693

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 REPLACEMENTTHROUGHOUT1LDG2.0129.752119220101109195.860.145210.145210.143110.18354RANDOM9.879
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]
-0.91-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.821
r_scangle_it4.273
r_scbond_it2.819
r_angle_refined_deg1.815
r_mcangle_it1.665
r_angle_other_deg1.646
r_mcbond_it0.985
r_symmetry_hbond_refined0.468
r_symmetry_vdw_other0.355
r_symmetry_vdw_refined0.293
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.821
r_scangle_it4.273
r_scbond_it2.819
r_angle_refined_deg1.815
r_mcangle_it1.665
r_angle_other_deg1.646
r_mcbond_it0.985
r_symmetry_hbond_refined0.468
r_symmetry_vdw_other0.355
r_symmetry_vdw_refined0.293
r_nbd_other0.233
r_nbd_refined0.206
r_xyhbond_nbd_refined0.141
r_chiral_restr0.102
r_nbtor_other0.083
r_gen_planes_other0.039
r_gen_planes_refined0.027
r_bond_refined_d0.024
r_bond_other_d0.012
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2383
Nucleic Acid Atoms
Solvent Atoms225
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing