2A92

Crystal structure of lactate dehydrogenase from Plasmodium vivax: complex with NADH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1T2CPDB Entry 1T2C

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.1291PEG 5000 monoethylether, Ammonium Sulphate, Mes, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3948.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.593α = 90
b = 128.636β = 90
c = 130.58γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-11-24MSINGLE 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
1291.2998.20.10811.83.99820498204226.95
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.197.597.30.4342.43.89639

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 1T2C2.0491.299014885849429997.820.1970.1970.1940.236RANDOM9.716
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]
1.44-1.850.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.529
r_dihedral_angle_3_deg14.824
r_dihedral_angle_4_deg14.051
r_dihedral_angle_1_deg7.112
r_scangle_it2.752
r_scbond_it1.9
r_angle_refined_deg1.525
r_mcangle_it1.08
r_mcbond_it0.721
r_nbtor_refined0.296
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.529
r_dihedral_angle_3_deg14.824
r_dihedral_angle_4_deg14.051
r_dihedral_angle_1_deg7.112
r_scangle_it2.752
r_scbond_it1.9
r_angle_refined_deg1.525
r_mcangle_it1.08
r_mcbond_it0.721
r_nbtor_refined0.296
r_symmetry_vdw_refined0.209
r_nbd_refined0.201
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.146
r_chiral_restr0.108
r_bond_refined_d0.015
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9596
Nucleic Acid Atoms
Solvent Atoms480
Heterogen Atoms176

Software

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