5IXS | pdb_00005ixs

Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 9: (6R)-3-[(2-chlorophenyl)sulfanyl]-4-hydroxy-6-(3-hydroxyphenyl)-6-(thiophen-3-yl)-5,6-dihydropyridin-2(1H)-one


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I10 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7292PEG 3350, sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.1542.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.624α = 90
b = 81.229β = 97.56
c = 104.797γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS 6M2012-07-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-10.9795SSRLBL11-1

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
12.0537.898.20.05816.63.5-332.7
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)
12.052.1280.5992.13.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1I102.0537.874896157198.010.174580.173590.180.22070.22RANDOM38.512
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]
-0.54-1.180.770.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.778
r_dihedral_angle_4_deg17.973
r_dihedral_angle_3_deg13.258
r_long_range_B_other11.591
r_long_range_B_refined11.537
r_scangle_other10.746
r_scbond_it8.338
r_scbond_other8.3
r_mcangle_other7.921
r_mcangle_it7.916
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.778
r_dihedral_angle_4_deg17.973
r_dihedral_angle_3_deg13.258
r_long_range_B_other11.591
r_long_range_B_refined11.537
r_scangle_other10.746
r_scbond_it8.338
r_scbond_other8.3
r_mcangle_other7.921
r_mcangle_it7.916
r_mcbond_it6.374
r_mcbond_other6.348
r_dihedral_angle_1_deg5.432
r_angle_refined_deg1.351
r_angle_other_deg0.778
r_chiral_restr0.145
r_gen_planes_refined0.018
r_gen_planes_other0.014
r_bond_refined_d0.007
r_bond_other_d0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10118
Nucleic Acid Atoms
Solvent Atoms569
Heterogen Atoms353

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing