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Protonation-mediated structural flexibility in the F conjugation regulatory protein, TraM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 297 30% PEG 400, 0.1M MES pH 6.5, 2mM DTT, 0.5M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 297K
Crystal Properties Matthews coefficient Solvent content 2.08 40.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.733 α = 90 b = 51.733 β = 90 c = 49.585 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 105 CCD ADSC QUANTUM 210 2005-06-14 M SINGLE WAVELENGTH 2 1 x-ray 105 CCD ADSC QUANTUM 210 2005-07-20 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11697 ALS 8.3.1 2 SYNCHROTRON ALS BEAMLINE 8.3.1 0.979617, 1.019440 ALS 8.3.1
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 1.4 36.58 99.1 0.039 27.6 3.6 12828 12828
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 1.4 1.42 86.6 86.6 0.371 3.12 2.8 548
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD THROUGHOUT 1.4 36.58 12827 12827 626 99.43 0.195 0.195 0.193 0.228 0.224 0.2627 RANDOM 17.335
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] -0.03 -0.03 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.961 r_dihedral_angle_4_deg 28.655 r_dihedral_angle_3_deg 10.366 r_dihedral_angle_1_deg 3.684 r_scangle_it 3.528 r_scbond_it 2.233 r_mcangle_it 1.243 r_angle_refined_deg 1.233 r_mcbond_it 0.744 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.961 r_dihedral_angle_4_deg 28.655 r_dihedral_angle_3_deg 10.366 r_dihedral_angle_1_deg 3.684 r_scangle_it 3.528 r_scbond_it 2.233 r_mcangle_it 1.243 r_angle_refined_deg 1.233 r_mcbond_it 0.744 r_nbtor_refined 0.307 r_nbd_refined 0.218 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.14 r_symmetry_hbond_refined 0.123 r_chiral_restr 0.081 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 544 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction