2BK6

The X-ray crystal structure of the Listeria innocua H31G Dps mutant.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1PEG 1000 15-30 % W/V, ACETATE BUFFERS IN A PH RANGE BETWEEN 5.0-6.5
Crystal Properties
Matthews coefficientSolvent content
2.5651.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 136.33α = 90
b = 136.33β = 90
c = 242.489γ = 90
Symmetry
Space GroupI 41 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONELETTRA BEAMLINE 5.2RELETTRA5.2R

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
12.24097.70.115657503
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.22.2898.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1QGH2.19119.5254615288397.30.2120.2110.231RANDOM27.39
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.455
r_dihedral_angle_4_deg15.505
r_dihedral_angle_3_deg15.406
r_dihedral_angle_1_deg3.567
r_angle_refined_deg1.909
r_scangle_it1.599
r_mcangle_it1.552
r_scbond_it1.113
r_mcbond_it1.005
r_nbtor_refined0.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.455
r_dihedral_angle_4_deg15.505
r_dihedral_angle_3_deg15.406
r_dihedral_angle_1_deg3.567
r_angle_refined_deg1.909
r_scangle_it1.599
r_mcangle_it1.552
r_scbond_it1.113
r_mcbond_it1.005
r_nbtor_refined0.271
r_symmetry_hbond_refined0.174
r_nbd_refined0.167
r_symmetry_vdw_refined0.165
r_chiral_restr0.161
r_xyhbond_nbd_refined0.11
r_bond_refined_d0.016
r_gen_planes_refined0.007
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7308
Nucleic Acid Atoms
Solvent Atoms546
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing