2FRD

Structure of Transhydrogenase (dI.S138A.NADH)2(dIII.NADPH)1 asymmetric complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1HZZpdb entry 1HZZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP627722-24% 8K-PEG, 60-140 mM (NH4)2SO4, 100 mM Mes, pH 6.0 and 10% glycerol in the presence of 50 mM NADH and 5 mM NADPH, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6553.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.3α = 90
b = 74.11β = 90
c = 205.22γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-02-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-10.934ESRFID14-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
13.245.9398.90.0720.07213.43.91840018400275.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
13.23.3799.20.32643.92660

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1HZZ3.245.9321671216712164398.40.218520.218520.213380.2723from pdb entry 1NM543.582
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]
0.634.27-4.9
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.804
r_dihedral_angle_3_deg15.681
r_dihedral_angle_4_deg13.878
r_dihedral_angle_1_deg6.894
r_scangle_it2.66
r_angle_other_deg2.001
r_scbond_it1.642
r_mcangle_it1.447
r_angle_refined_deg1.217
r_mcbond_it1.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.804
r_dihedral_angle_3_deg15.681
r_dihedral_angle_4_deg13.878
r_dihedral_angle_1_deg6.894
r_scangle_it2.66
r_angle_other_deg2.001
r_scbond_it1.642
r_mcangle_it1.447
r_angle_refined_deg1.217
r_mcbond_it1.103
r_symmetry_hbond_refined0.169
r_nbd_other0.168
r_nbd_refined0.163
r_xyhbond_nbd_refined0.159
r_nbtor_refined0.158
r_symmetry_vdw_other0.121
r_nbtor_other0.079
r_symmetry_vdw_refined0.078
r_chiral_restr0.059
r_mcbond_other0.044
r_xyhbond_nbd_other0.034
r_gen_planes_other0.031
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6619
Nucleic Acid Atoms
Solvent Atoms2
Heterogen Atoms136

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling