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N-terminal GAF domain of transcriptional pleiotropic repressor CodY
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2B18 PDB ENTRY 2B18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 291 ammonium sulphate, sodium citrate, PEG 400, 20mM cGMP, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.71 54.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.207 α = 90 b = 90.207 β = 90 c = 205.634 γ = 90
Symmetry Space Group P 43 2 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 CCD ADSC QUANTUM 315 2005-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.97570 ESRF ID23-1
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 1.74 50 98 0.083 22.11 7.2 85808 85808 26.6
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 1.74 1.8 95.2 0.612 1.67 3.7 8202
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 PDB ENTRY 2B18 1.74 31.89 79437 79437 4191 97.46 0.18872 0.18872 0.18726 0.1936 0.21595 0.1937 RANDOM 23.72
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] -0.21 -0.21 0.42
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.992 r_dihedral_angle_4_deg 16.115 r_dihedral_angle_3_deg 15.72 r_dihedral_angle_1_deg 5.412 r_scangle_it 5.221 r_scbond_it 3.879 r_mcangle_it 3.416 r_rigid_bond_restr 3.407 r_sphericity_free 3.097 r_mcbond_it 2.622
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.992 r_dihedral_angle_4_deg 16.115 r_dihedral_angle_3_deg 15.72 r_dihedral_angle_1_deg 5.412 r_scangle_it 5.221 r_scbond_it 3.879 r_mcangle_it 3.416 r_rigid_bond_restr 3.407 r_sphericity_free 3.097 r_mcbond_it 2.622 r_sphericity_bonded 2.21 r_mcbond_other 1.092 r_angle_refined_deg 1.076 r_angle_other_deg 0.855 r_symmetry_vdw_other 0.222 r_symmetry_vdw_refined 0.218 r_nbd_refined 0.208 r_nbd_other 0.184 r_nbtor_refined 0.166 r_xyhbond_nbd_refined 0.134 r_symmetry_hbond_refined 0.122 r_nbtor_other 0.086 r_chiral_restr 0.07 r_xyhbond_nbd_other 0.026 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5039 Nucleic Acid Atoms Solvent Atoms 388 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement ADSC data collection HKL-2000 data scaling MOLREP phasing