2OO5

Structure of transhydrogenase (dI.H2NADH)2(dIII.NADP+)1 asymmetric complex


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1U2DPDB ENTRY 1U2D

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION827718% PEG 4000, 10% glycerol, 100mM Tris, 75mM lithium sulphate, VAPOR DIFFUSION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.3848.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.199α = 90
b = 101.025β = 90
c = 131.721γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-30.93100ESRFID14-3

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
12.680.16392.80.0730.0737.73.827548
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.62.7494.40.2270.2273.33.14046

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1U2D2.680.0627507139691.90.2220.2190.275RANDOM38.228
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]
-0.34-0.911.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.147
r_dihedral_angle_3_deg14.661
r_dihedral_angle_4_deg14.041
r_dihedral_angle_1_deg7.606
r_angle_refined_deg1.252
r_mcangle_it1.149
r_mcbond_it0.974
r_scangle_it0.97
r_angle_other_deg0.934
r_scbond_it0.619
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.147
r_dihedral_angle_3_deg14.661
r_dihedral_angle_4_deg14.041
r_dihedral_angle_1_deg7.606
r_angle_refined_deg1.252
r_mcangle_it1.149
r_mcbond_it0.974
r_scangle_it0.97
r_angle_other_deg0.934
r_scbond_it0.619
r_nbtor_refined0.147
r_nbd_refined0.142
r_mcbond_other0.135
r_xyhbond_nbd_refined0.127
r_nbd_other0.124
r_symmetry_vdw_other0.108
r_symmetry_hbond_refined0.095
r_nbtor_other0.079
r_chiral_restr0.064
r_symmetry_vdw_refined0.063
r_bond_refined_d0.008
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6899
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms156

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
CCP4data scaling