1O94

Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2TMDPDB ENTRY 2TMD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.58% PEG 20000, 8% PEG 750 MME, 0.1-0.3 M SODIUM ACETATE, pH 6.50
Crystal Properties
Matthews coefficientSolvent content
2.7154.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.93α = 90
b = 211.543β = 100.03
c = 125.97γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCD2002-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.6SRSPX9.6

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
122094.80.07111.53.2184949
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)
122.0589.50.2512.9

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 2TMD219.8818494998111000.1740.1720.212RANDOM33.33
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]
2.74-0.65-1.76-1.21
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.399
r_dihedral_angle_4_deg19.273
r_dihedral_angle_3_deg15.579
r_dihedral_angle_1_deg6.988
r_scangle_it4.844
r_scbond_it3.153
r_angle_other_deg1.975
r_mcangle_it1.749
r_mcbond_it1.017
r_symmetry_vdw_refined0.377
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.399
r_dihedral_angle_4_deg19.273
r_dihedral_angle_3_deg15.579
r_dihedral_angle_1_deg6.988
r_scangle_it4.844
r_scbond_it3.153
r_angle_other_deg1.975
r_mcangle_it1.749
r_mcbond_it1.017
r_symmetry_vdw_refined0.377
r_nbd_refined0.235
r_symmetry_hbond_refined0.19
r_xyhbond_nbd_refined0.175
r_chiral_restr0.144
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_bond_other_d
r_angle_refined_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms17598
Nucleic Acid Atoms
Solvent Atoms2149
Heterogen Atoms178

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing