4ZVV

Lactate dehydrogenase A in complex with a trisubstituted piperidine-2,4-dione inhibitor GNE-140


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7293PEG3350, malonate pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.2344

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.164α = 90
b = 81.288β = 98.31
c = 102.47γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110CCDADSC QUANTUM 315r2013-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.9793SSRFBL17U

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
12.238.4599.30.0913.63.75612956050-333.05

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1I102.238.4556050115299.20.232680.23210.25947RANDOM35.723
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]
-0.16-0.860.68-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.921
r_dihedral_angle_4_deg18.909
r_dihedral_angle_3_deg14.827
r_dihedral_angle_1_deg4.655
r_scangle_it1.589
r_angle_refined_deg1.136
r_scbond_it1.08
r_mcangle_it0.739
r_mcbond_it0.455
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.921
r_dihedral_angle_4_deg18.909
r_dihedral_angle_3_deg14.827
r_dihedral_angle_1_deg4.655
r_scangle_it1.589
r_angle_refined_deg1.136
r_scbond_it1.08
r_mcangle_it0.739
r_mcbond_it0.455
r_chiral_restr0.085
r_bond_refined_d0.012
r_gen_planes_refined0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10271
Nucleic Acid Atoms
Solvent Atoms309
Heterogen Atoms343

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing