7DBJ

Crystal structure of human LDHB in complex with NADH, oxamate, and AXKO-0046


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I0Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5293PEG 3350, potassium formate, HEPES
Crystal Properties
Matthews coefficientSolvent content
2.2445.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.389α = 90
b = 137.577β = 109.264
c = 84.909γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2019-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSPRING-8 BEAMLINE BL45XU1SPring-8BL45XU

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rpim 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
11.555099.20.0760.0420.98920.34.1183405
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.5893.80.2510.1490.92343.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE1I0Z1.55143.496183364914698.9230.1710.16970.191723.8
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]
-0.5340.2320.0490.26
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.144
r_dihedral_angle_4_deg19.508
r_dihedral_angle_3_deg11.901
r_dihedral_angle_1_deg6.418
r_lrange_it3.065
r_lrange_other3.058
r_angle_other_deg1.6
r_dihedral_angle_other_2_deg1.576
r_angle_refined_deg1.549
r_scangle_it1.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.144
r_dihedral_angle_4_deg19.508
r_dihedral_angle_3_deg11.901
r_dihedral_angle_1_deg6.418
r_lrange_it3.065
r_lrange_other3.058
r_angle_other_deg1.6
r_dihedral_angle_other_2_deg1.576
r_angle_refined_deg1.549
r_scangle_it1.247
r_scangle_other1.247
r_scbond_it0.969
r_scbond_other0.969
r_mcangle_it0.806
r_mcangle_other0.806
r_mcbond_it0.642
r_mcbond_other0.64
r_nbd_other0.263
r_nbd_refined0.208
r_symmetry_nbd_other0.186
r_symmetry_nbd_refined0.177
r_nbtor_refined0.163
r_symmetry_xyhbond_nbd_refined0.152
r_xyhbond_nbd_refined0.113
r_chiral_restr0.083
r_symmetry_nbtor_other0.074
r_bond_refined_d0.011
r_bond_other_d0.011
r_gen_planes_refined0.01
r_gen_planes_other0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10244
Nucleic Acid Atoms
Solvent Atoms765
Heterogen Atoms284

Software

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