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The structure of the cofactor binding GAF domain of the nutrient sensor CodY from Clostridium difficile
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 20% polyethylene glycol 3350, 0.2 M sodium formate, 0.1 M Bis-tris-propane, pH 6.5 and protein solutions containing 10 mM isoleucine.
Crystal Properties Matthews coefficient Solvent content 2.4 48.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.89 α = 90 b = 190.39 β = 90 c = 43.51 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2015-01-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.97949 Diamond I02
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.68 56.19 100 0.067 0.999 17.1 8.1 115569
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.68 1.72 99.9 1.81 0.515 8.1
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 2B18 1.68 56.19 109833 5726 99.96 0.15778 0.15406 0.1643 0.2283 0.2335 RANDOM 37.644
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] 0.79 -0.39 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.489 r_sphericity_free 35.621 r_sphericity_bonded 25.944 r_dihedral_angle_3_deg 15.788 r_dihedral_angle_4_deg 11.415 r_dihedral_angle_1_deg 9.683 r_scangle_other 8.695 r_long_range_B_refined 8.694 r_long_range_B_other 8.652 r_scbond_it 7.723
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.489 r_sphericity_free 35.621 r_sphericity_bonded 25.944 r_dihedral_angle_3_deg 15.788 r_dihedral_angle_4_deg 11.415 r_dihedral_angle_1_deg 9.683 r_scangle_other 8.695 r_long_range_B_refined 8.694 r_long_range_B_other 8.652 r_scbond_it 7.723 r_scbond_other 7.723 r_mcangle_it 7.591 r_mcangle_other 7.59 r_mcbond_other 6.31 r_mcbond_it 6.309 r_rigid_bond_restr 5.349 r_angle_refined_deg 2.538 r_angle_other_deg 1.319 r_chiral_restr 0.151 r_bond_refined_d 0.027 r_gen_planes_refined 0.011 r_bond_other_d 0.003 r_gen_planes_other 0.003 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_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7230 Nucleic Acid Atoms Solvent Atoms 648 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing