6SBV

X-ray Structure of Human LDH-A with an Allosteric Inhibitor (Compound 7)


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
3.0960.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 80.369α = 90
b = 146.287β = 90
c = 308.362γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-07-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

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
12.65099.50.2250.9916.185.4112371
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)
12.62.7698.70.8610.7971.635.4

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 REPLACEMENTTHROUGHOUT4l4r2.648.93110270210199.540.219540.21910.24233RANDOM43.504
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]
4.22-0.08-4.14
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.609
r_dihedral_angle_4_deg21.366
r_dihedral_angle_3_deg15.71
r_dihedral_angle_1_deg6.635
r_long_range_B_refined6.347
r_long_range_B_other6.344
r_scangle_other4.545
r_mcangle_it3.767
r_mcangle_other3.767
r_scbond_it2.729
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.609
r_dihedral_angle_4_deg21.366
r_dihedral_angle_3_deg15.71
r_dihedral_angle_1_deg6.635
r_long_range_B_refined6.347
r_long_range_B_other6.344
r_scangle_other4.545
r_mcangle_it3.767
r_mcangle_other3.767
r_scbond_it2.729
r_scbond_other2.728
r_mcbond_it2.35
r_mcbond_other2.35
r_angle_refined_deg1.287
r_angle_other_deg1.161
r_chiral_restr0.052
r_bond_refined_d0.005
r_gen_planes_refined0.004
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 Atoms20374
Nucleic Acid Atoms
Solvent Atoms391
Heterogen Atoms264

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building