3AK9 | pdb_00003ak9

Crystal structure of the SEp22 dodecamer, a Dps-like protein from Salmonella enterica subsp. enterica serovar Enteritidis, FE-soaked form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3AK8PDB ENTRY 3AK8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.3293Reservoir 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 coefficientSolvent content
2.1442.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.471α = 90
b = 98.003β = 90
c = 208.414γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 315r2009-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-5A1.0000Photon FactoryBL-5A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.348.690.850.06117.84.144840740737828.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.31.3389.40.3962.42.831051

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3AK81.348.64073784073782151190.850.15360.15360.15260.160.17230.18RANDOM25.381
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]
-0.050.010.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.043
r_dihedral_angle_4_deg19.468
r_dihedral_angle_3_deg12.715
r_scangle_it4.643
r_dihedral_angle_1_deg4.578
r_scbond_it3.165
r_mcangle_it2.026
r_rigid_bond_restr1.382
r_angle_refined_deg1.244
r_mcbond_it1.233
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.043
r_dihedral_angle_4_deg19.468
r_dihedral_angle_3_deg12.715
r_scangle_it4.643
r_dihedral_angle_1_deg4.578
r_scbond_it3.165
r_mcangle_it2.026
r_rigid_bond_restr1.382
r_angle_refined_deg1.244
r_mcbond_it1.233
r_chiral_restr0.084
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 AtomsNumber
Protein Atoms14764
Nucleic Acid Atoms
Solvent Atoms1321
Heterogen Atoms46

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling