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Protonation-mediated structural flexibility in the F conjugation regulatory protein, TRAM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G7O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 295 30% PEG 400, 0.1M MES PH 6.5, 2MM DTT, 0.5M AMMONIUM ACETATE , pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 1.9 35.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.939 α = 90 b = 50.939 β = 90 c = 46.551 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 2005-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 1.11587 ALS 8.3.1
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 36.01 98.6 0.045 0.047 25.1 3.6 5552 5552
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) Redundancy Number Unique Reflections (All) 1 1.8 1.83 84.1 0.362 0.363 2.38 2.2 232
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 (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 MOLECULAR REPLACEMENT THROUGHOUT 2G7O 1.8 36.01 5288 5288 262 98.65 0.18511 0.18511 0.18231 0.1815 0.24459 0.244 RANDOM 23.832
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] -0.5 -0.5 1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.931 r_dihedral_angle_4_deg 25.767 r_dihedral_angle_3_deg 13.087 r_dihedral_angle_1_deg 4.777 r_scangle_it 2.978 r_scbond_it 1.842 r_angle_refined_deg 1.193 r_mcangle_it 1.023 r_mcbond_it 0.565 r_nbtor_refined 0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.931 r_dihedral_angle_4_deg 25.767 r_dihedral_angle_3_deg 13.087 r_dihedral_angle_1_deg 4.777 r_scangle_it 2.978 r_scbond_it 1.842 r_angle_refined_deg 1.193 r_mcangle_it 1.023 r_mcbond_it 0.565 r_nbtor_refined 0.3 r_symmetry_vdw_refined 0.205 r_nbd_refined 0.204 r_symmetry_hbond_refined 0.172 r_xyhbond_nbd_refined 0.118 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 543 Nucleic Acid Atoms Solvent Atoms 42 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling MOLREP phasing