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Ternary complex between trimethylamine dehydrogenase and electron transferring flavoprotein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2TMD PDB ENTRY 2TMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 8% PEG 20000, 8% PEG 750 MME, 0.1-0.3 M SODIUM ACETATE, pH 6.50
Crystal Properties Matthews coefficient Solvent content 2.71 54.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.93 α = 90 b = 211.543 β = 100.03 c = 125.97 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD 2002-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX9.6 SRS PX9.6
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2 20 94.8 0.071 11.5 3.2 184949
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.05 89.5 0.251 2.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2TMD 2 19.88 184949 9811 100 0.174 0.172 0.1753 0.212 0.2125 RANDOM 33.33
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 Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.399 r_dihedral_angle_4_deg 19.273 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_1_deg 6.988 r_scangle_it 4.844 r_scbond_it 3.153 r_angle_other_deg 1.975 r_mcangle_it 1.749 r_mcbond_it 1.017 r_symmetry_vdw_refined 0.377
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.399 r_dihedral_angle_4_deg 19.273 r_dihedral_angle_3_deg 15.579 r_dihedral_angle_1_deg 6.988 r_scangle_it 4.844 r_scbond_it 3.153 r_angle_other_deg 1.975 r_mcangle_it 1.749 r_mcbond_it 1.017 r_symmetry_vdw_refined 0.377 r_nbd_refined 0.235 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.175 r_chiral_restr 0.144 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 Atoms Number Protein Atoms 17598 Nucleic Acid Atoms Solvent Atoms 2149 Heterogen Atoms 178
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing