7M2N

Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5W8J 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2910.2 M Lithium Sulfate, 0.1 M Sodium Cacodylate pH 6.5, 30% (v/v) PEG 400
Crystal Properties
Matthews coefficientSolvent content
4.0169.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.93α = 90
b = 131.05β = 99.3
c = 215.518γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 200K2019-11-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.5501000.10413.464.678979
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.540.87

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 REPLACEMENTTHROUGHOUT5W8J2.548.8974825391097.60.211750.209380.25769RANDOM37.906
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]
-0.010.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.778
r_dihedral_angle_4_deg25.207
r_dihedral_angle_3_deg15.5
r_long_range_B_other7.559
r_long_range_B_refined7.556
r_dihedral_angle_1_deg6.588
r_scangle_other5.585
r_mcangle_it4.313
r_mcangle_other4.313
r_scbond_it3.669
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.778
r_dihedral_angle_4_deg25.207
r_dihedral_angle_3_deg15.5
r_long_range_B_other7.559
r_long_range_B_refined7.556
r_dihedral_angle_1_deg6.588
r_scangle_other5.585
r_mcangle_it4.313
r_mcangle_other4.313
r_scbond_it3.669
r_scbond_other3.669
r_mcbond_it2.936
r_mcbond_other2.935
r_angle_refined_deg1.461
r_angle_other_deg1.231
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.006
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 Atoms10170
Nucleic Acid Atoms
Solvent Atoms537
Heterogen Atoms808

Software

Software
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing