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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 7 291 PEG 5000, calcium acetate, valine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.15 42.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.69 α = 90 b = 84.846 β = 90 c = 54.929 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 CCD MARMOSAIC 225 mm CCD 2005-04-25 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.9800 ESRF BM14
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 2.3 30 99 0.104 13.7 6.1 7646 7646
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) 2.3 2.38 92.2 0.361 4.2 672
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 2.3 27.72 7231 7231 350 100 0.16804 0.16804 0.16427 0.1805 0.24418 0.2585 RANDOM 39.09
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] -0.01 0.18 -0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.5 r_dihedral_angle_4_deg 16.204 r_dihedral_angle_3_deg 15.735 r_dihedral_angle_1_deg 5.821 r_scangle_it 5.367 r_sphericity_free 4.256 r_scbond_it 3.738 r_mcangle_it 3.701 r_mcbond_it 2.83 r_sphericity_bonded 1.901
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.5 r_dihedral_angle_4_deg 16.204 r_dihedral_angle_3_deg 15.735 r_dihedral_angle_1_deg 5.821 r_scangle_it 5.367 r_sphericity_free 4.256 r_scbond_it 3.738 r_mcangle_it 3.701 r_mcbond_it 2.83 r_sphericity_bonded 1.901 r_rigid_bond_restr 1.677 r_angle_refined_deg 1.408 r_mcbond_other 0.858 r_angle_other_deg 0.819 r_symmetry_hbond_refined 0.251 r_symmetry_vdw_other 0.249 r_symmetry_vdw_refined 0.221 r_nbd_refined 0.209 r_nbd_other 0.196 r_xyhbond_nbd_refined 0.193 r_nbtor_refined 0.17 r_nbtor_other 0.087 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other 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 1236 Nucleic Acid Atoms Solvent Atoms 131 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing