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Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis, FE-soaked form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3AK8 PDB ENTRY 3AK8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.3 293 Reservoir solution: 0.1M sodium acetate, 0.3M magnesium chloride, 28% PEG 400. The crystal was soaked in the solution containing 0.1M MES pH6.0, 0.25M magnesium chloride, 30% PEG 400, 0.1M ascorbic acid, and 0.1M ferrous ammonium sulfate., pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.14 42.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 94.471 α = 90 b = 98.003 β = 90 c = 208.414 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 315r 2009-06-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.3 48.6 90.85 0.061 17.8 4.1 448407 407378 28.3
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) 1.3 1.33 89.4 0.396 2.4 2.8 31051
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 3AK8 1.3 48.6 407378 407378 21511 90.85 0.1536 0.1536 0.1526 0.161 0.1723 0.1806 RANDOM 25.381
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] -0.05 0.01 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.043 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_3_deg 12.715 r_scangle_it 4.643 r_dihedral_angle_1_deg 4.578 r_scbond_it 3.165 r_mcangle_it 2.026 r_rigid_bond_restr 1.382 r_angle_refined_deg 1.244 r_mcbond_it 1.233
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.043 r_dihedral_angle_4_deg 19.468 r_dihedral_angle_3_deg 12.715 r_scangle_it 4.643 r_dihedral_angle_1_deg 4.578 r_scbond_it 3.165 r_mcangle_it 2.026 r_rigid_bond_restr 1.382 r_angle_refined_deg 1.244 r_mcbond_it 1.233 r_chiral_restr 0.084 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14764 Nucleic Acid Atoms Solvent Atoms 1321 Heterogen Atoms 46
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling