1T2F

Human B lactate dehydrogenase complexed with NAD+ and 4-hydroxy-1,2,5-oxadiazole-3-carboxylic acid


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291PEG 4000, Ammonium acetate, Na citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.1850

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 137.397α = 90
b = 160.443β = 90
c = 59.366γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMACSCIENCE2001-07-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEENRAF-NONIUS FR5911.5418

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
13300.1666.42.7272142474222
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)
33.1679.10.3022.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1IOZ329.882447423299124290.520.22060.215270.32053RANDOM52.254
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]
-2.422.71-0.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.001
r_scangle_it2.668
r_angle_refined_deg2.017
r_scbond_it1.554
r_angle_other_deg1.381
r_mcangle_it1.161
r_mcbond_it0.633
r_symmetry_vdw_other0.332
r_symmetry_vdw_refined0.311
r_symmetry_hbond_refined0.275
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg9.001
r_scangle_it2.668
r_angle_refined_deg2.017
r_scbond_it1.554
r_angle_other_deg1.381
r_mcangle_it1.161
r_mcbond_it0.633
r_symmetry_vdw_other0.332
r_symmetry_vdw_refined0.311
r_symmetry_hbond_refined0.275
r_nbd_refined0.266
r_xyhbond_nbd_refined0.258
r_nbd_other0.254
r_xyhbond_nbd_other0.202
r_chiral_restr0.118
r_nbtor_other0.092
r_symmetry_hbond_other0.084
r_bond_refined_d0.02
r_gen_planes_refined0.006
r_gen_planes_other0.003
r_bond_other_d0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_refined
r_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10220
Nucleic Acid Atoms
Solvent Atoms233
Heterogen Atoms212

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing