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C-terminal DNA binding domain of transcriptional pleiotropic repressor CodY.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 291 ammoium sulphate, sodium citrate, NaCl, glycerol, tacsimate, TRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.9 56.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.128 α = 90 b = 68.128 β = 90 c = 164.903 γ = 90
Symmetry Space Group P 4 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 298 IMAGE PLATE MARRESEARCH Blue Osmics 2005-08-12 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315r 2005-02-12 M MAD 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178 2 SYNCHROTRON ESRF BEAMLINE ID23-1 0.978, 0.975, 0.978 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 1,2 2.9 25 94.4 0.072 15.4 3.7 8705 8705
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 2.9 2.974 84.3 0.655 1.2 2.4 758
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 2.9 10 8018 8018 393 100 0.20445 0.20445 0.20215 0.2122 0.25033 0.2584 RANDOM 74.163
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] -0.22 -0.22 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.888 r_dihedral_angle_3_deg 23.582 r_dihedral_angle_4_deg 17.915 r_scangle_it 9.24 r_dihedral_angle_1_deg 7.702 r_scbond_it 6.356 r_mcangle_it 5.127 r_mcbond_it 3.262 r_angle_refined_deg 1.544 r_nbtor_refined 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.888 r_dihedral_angle_3_deg 23.582 r_dihedral_angle_4_deg 17.915 r_scangle_it 9.24 r_dihedral_angle_1_deg 7.702 r_scbond_it 6.356 r_mcangle_it 5.127 r_mcbond_it 3.262 r_angle_refined_deg 1.544 r_nbtor_refined 0.31 r_symmetry_vdw_refined 0.302 r_nbd_refined 0.268 r_xyhbond_nbd_refined 0.182 r_symmetry_hbond_refined 0.159 r_chiral_restr 0.103 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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 2234 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling HKL2Map phasing