6SBU

X-ray Structure of Human LDHA with an Allosteric Inhibitor (Compound 3)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2930.1 M HEPES pH 7.5-7.7, 4-8% PEG 8000, 20% ethylene glycol, and 10% acetonitrile
Crystal Properties
Matthews coefficientSolvent content
2.9958.91

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.445α = 90
b = 143.853β = 90
c = 311.225γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-04-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-10.975656ESRFID23-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rrim I (All)CC (Half)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
12.9150990.1560.9959.144.477153
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.913.0996.91.0780.7731.854.6

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 REPLACEMENTTHROUGHOUT4L4R2.9148.875038210098.980.208480.207490.24447RANDOM63.2
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]
3.850.54-4.38
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.647
r_dihedral_angle_4_deg24.011
r_dihedral_angle_3_deg17.426
r_long_range_B_other10.114
r_long_range_B_refined10.113
r_scangle_other7.886
r_dihedral_angle_1_deg6.933
r_mcangle_it6.851
r_mcangle_other6.85
r_scbond_it5.019
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.647
r_dihedral_angle_4_deg24.011
r_dihedral_angle_3_deg17.426
r_long_range_B_other10.114
r_long_range_B_refined10.113
r_scangle_other7.886
r_dihedral_angle_1_deg6.933
r_mcangle_it6.851
r_mcangle_other6.85
r_scbond_it5.019
r_scbond_other5
r_mcbond_it4.515
r_mcbond_other4.514
r_angle_refined_deg1.444
r_angle_other_deg1.165
r_chiral_restr0.051
r_bond_refined_d0.006
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
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 Atoms20320
Nucleic Acid Atoms
Solvent Atoms92
Heterogen Atoms328

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building