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Crystal structure of a possible transciptional regulator YggD from Shigella flexneri 2a str. 2457T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 30% (w/v) PEG MME 2000, 0.1M Sodium acetate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.53 51.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.365 α = 90 b = 70.946 β = 90.43 c = 159.037 γ = 90
Symmetry Space Group C 1 2 1
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 SBC-3 Mirrors 2006-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97883 APS 19-BM
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 2.5 32 94.2 0.074 30.78 4 26162 26162 71.63
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 2.5 2.59 78.9 0.52 1.88 3.2 2140
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 2.5 31.81 24064 24064 2020 93.92 0.21163 0.21163 0.20669 0.27034 0.2708 RANDOM 63.751
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] -0.3 -0.27 0.13 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.817 r_dihedral_angle_4_deg 23.332 r_dihedral_angle_3_deg 22.759 r_dihedral_angle_1_deg 6.195 r_scangle_it 2.881 r_scbond_it 1.877 r_angle_refined_deg 1.721 r_mcangle_it 1.223 r_mcbond_it 0.739 r_nbtor_refined 0.322
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.817 r_dihedral_angle_4_deg 23.332 r_dihedral_angle_3_deg 22.759 r_dihedral_angle_1_deg 6.195 r_scangle_it 2.881 r_scbond_it 1.877 r_angle_refined_deg 1.721 r_mcangle_it 1.223 r_mcbond_it 0.739 r_nbtor_refined 0.322 r_symmetry_vdw_refined 0.252 r_nbd_refined 0.246 r_symmetry_hbond_refined 0.171 r_xyhbond_nbd_refined 0.137 r_chiral_restr 0.126 r_bond_refined_d 0.014 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 5334 Nucleic Acid Atoms Solvent Atoms 12 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling SHELXD phasing MLPHARE phasing DM phasing RESOLVE phasing HKL-3000 phasing