2AA3

Crystal structure of Plasmodium vivax lactate dehydrogenase complex with APADH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2A92PDB Entry 2A92

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5291PEG5k MME, Ammonium sulphate, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3747.75

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.482α = 90
b = 128.454β = 90
c = 130.781γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42005-04-18MSINGLE 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 Merge 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
12.0591.6798.40.09921.38.28549985499227.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.052.1296.996.90.3790.3794.67.8

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 2A922.0591.678549985445427698.330.1920.1920.1910.226RANDOM20.838
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]
-0.16-0.450.61
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.455
r_dihedral_angle_3_deg14.906
r_dihedral_angle_4_deg14.822
r_dihedral_angle_1_deg6.528
r_scangle_it3.333
r_scbond_it2.4
r_angle_refined_deg1.783
r_mcangle_it1.457
r_mcbond_it0.95
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.455
r_dihedral_angle_3_deg14.906
r_dihedral_angle_4_deg14.822
r_dihedral_angle_1_deg6.528
r_scangle_it3.333
r_scbond_it2.4
r_angle_refined_deg1.783
r_mcangle_it1.457
r_mcbond_it0.95
r_nbtor_refined0.302
r_nbd_refined0.209
r_symmetry_vdw_refined0.181
r_xyhbond_nbd_refined0.138
r_chiral_restr0.126
r_symmetry_hbond_refined0.122
r_bond_refined_d0.022
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9637
Nucleic Acid Atoms
Solvent Atoms479
Heterogen Atoms186

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction