6BB0

Lactate Dehydrogenase in complex with inhibitor (R)-3-((2-chlorophenyl)thio)-6-(3-((4-fluorophenyl)amino)phenyl)-4-hydroxy-6-(thiophen-3-yl)-5,6-dihydro-2H-pyran-2-one


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7291PEG3350, sodium malonate
Crystal Properties
Matthews coefficientSolvent content
2.2144.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.125α = 90
b = 80.968β = 98.33
c = 103.214γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110PIXELDECTRIS PILATUS3 S 6M2012-07-12MSINGLE 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
11.953997.80.04616.63.491115-331
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)
11.952.0595.90.4912.33.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT1.9538.6589141183097.90.167530.166480.21507RANDOM37.916
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]
-1.27-1.472.2-0.48
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.653
r_dihedral_angle_4_deg21.211
r_scangle_other14.209
r_long_range_B_other13.945
r_long_range_B_refined13.924
r_scbond_other12.833
r_scbond_it12.811
r_dihedral_angle_3_deg12.758
r_mcangle_other9.331
r_mcangle_it9.325
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.653
r_dihedral_angle_4_deg21.211
r_scangle_other14.209
r_long_range_B_other13.945
r_long_range_B_refined13.924
r_scbond_other12.833
r_scbond_it12.811
r_dihedral_angle_3_deg12.758
r_mcangle_other9.331
r_mcangle_it9.325
r_mcbond_it8.645
r_mcbond_other8.598
r_dihedral_angle_1_deg5.713
r_angle_refined_deg1.509
r_angle_other_deg0.976
r_chiral_restr0.172
r_gen_planes_refined0.021
r_gen_planes_other0.017
r_bond_refined_d0.01
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 Atoms10065
Nucleic Acid Atoms
Solvent Atoms721
Heterogen Atoms334

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing