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Crystal structure of yciE protein from E. coli CFT073, a member of ferritine-like superfamily of diiron-containing four-helix-bundle proteins
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 25% Peg 3350, 0.2 M Magnesium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 1.96 37.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 30.148 α = 90 b = 90.295 β = 103.51 c = 58.132 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 315r mirrors 2010-02-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9794 APS 19-ID
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 1.65 40 99.8 0.083 29 3.7 36700 36634 2 2
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) 1.65 1.68 99.5 0.367 4 3.5 1843
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 SAD THROUGHOUT 1.65 40 36311 34496 1815 99.46 0.18 0.16878 0.16648 0.165 0.21291 0.2113 RANDOM 25.968
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] -0.14 -0.91 -1.96 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.453 r_dihedral_angle_3_deg 13.441 r_dihedral_angle_4_deg 10.732 r_scangle_it 6.65 r_mcbond_other 5.601 r_dihedral_angle_1_deg 4.869 r_scbond_it 4.221 r_mcangle_it 3.304 r_rigid_bond_restr 2.408 r_mcbond_it 1.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.453 r_dihedral_angle_3_deg 13.441 r_dihedral_angle_4_deg 10.732 r_scangle_it 6.65 r_mcbond_other 5.601 r_dihedral_angle_1_deg 4.869 r_scbond_it 4.221 r_mcangle_it 3.304 r_rigid_bond_restr 2.408 r_mcbond_it 1.88 r_angle_refined_deg 1.794 r_angle_other_deg 1.18 r_chiral_restr 0.115 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2353 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 5
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 phasing SHELX model building ARP/wARP model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling SHELX phasing