1XIV

Plasmodium falciparum lactate dehydrogenase complexed with 2-({4-chloro-[hydroxy(methoxy)methyl]cyclohexyl}amino)ethane-1,1,2-triol


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
2.4148.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.568α = 90
b = 85.393β = 90
c = 92.263γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH2001-05-21MSINGLE 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
11.73095.30.05823.24.5353173365722
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)
11.71.7892.20.2075.344018

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 1LDG1.729.363300931329168093.460.145610.145610.143870.17884RANDOM13.233
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]
-0.170.59-0.42
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.522
r_scangle_it3.877
r_scbond_it2.382
r_angle_refined_deg1.435
r_mcangle_it1.357
r_angle_other_deg1.242
r_mcbond_it0.752
r_nbd_refined0.33
r_symmetry_vdw_other0.301
r_nbd_other0.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.522
r_scangle_it3.877
r_scbond_it2.382
r_angle_refined_deg1.435
r_mcangle_it1.357
r_angle_other_deg1.242
r_mcbond_it0.752
r_nbd_refined0.33
r_symmetry_vdw_other0.301
r_nbd_other0.238
r_xyhbond_nbd_refined0.155
r_symmetry_hbond_refined0.148
r_symmetry_vdw_refined0.143
r_nbtor_other0.086
r_chiral_restr0.084
r_bond_refined_d0.015
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 Atoms2320
Nucleic Acid Atoms
Solvent Atoms360
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing