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Crystal structure of Treponema pallidum TP0796 Flavin trafficking protein, FAD substrate bound form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4IFU PDB ENTRY 4IFU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 hanging-drop vapor diffusion 6.5 293 0.1 M MES, 0.8 M sodium acetate, 0.1 M NaCl, 20% (w/v) ethylene glycol, pH 6.5, hanging-drop vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.825 α = 90 b = 47.079 β = 102 c = 57.583 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 ADSC QUANTUM 315r monochromator 2011-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 APS 19-ID
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 1.45 50 98.4 0.04 13.3 4 53215 53215 1 1
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 1.45 1.48 95.3 0.628 3.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 4IFU 1.452 28.58 53127 50440 2687 97.96 0.17391 0.17237 0.1719 0.20354 0.2027 RANDOM 24.954
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] 0.4 1.12 -0.22 -0.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.205 r_dihedral_angle_4_deg 17.578 r_dihedral_angle_3_deg 11.249 r_dihedral_angle_1_deg 6.682 r_angle_refined_deg 2.228 r_angle_other_deg 0.948 r_chiral_restr 0.142 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.205 r_dihedral_angle_4_deg 17.578 r_dihedral_angle_3_deg 11.249 r_dihedral_angle_1_deg 6.682 r_angle_refined_deg 2.228 r_angle_other_deg 0.948 r_chiral_restr 0.142 r_bond_refined_d 0.022 r_gen_planes_refined 0.011 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2521 Nucleic Acid Atoms Solvent Atoms 247 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PDB_EXTRACT data extraction HKL-3000 data collection DENZO data reduction HKL-3000 data scaling PHENIX phasing SCALEPACK data scaling