5A61

Crystal structure of full-length E. coli ygiF in complex with tripolyphosphate and two manganese ions.


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3,350, 0.2 M NACL
Crystal Properties
Matthews coefficientSolvent content
2.9958.88

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.676α = 90
b = 89.676β = 90
c = 125.329γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS2014-05-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.999990, 1.700020SLSX10SA

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
11.548.7799.80.0426.3515.4891340-3
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)
11.51.5999.11.342.0314.18

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 DIFFRACTIONOTHERTHROUGHOUTNONE1.548.778657345131000.152420.151450.17087RANDOM52.368
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]
0.380.190.38-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.73
r_sphericity_free26.526
r_sphericity_bonded14.418
r_dihedral_angle_4_deg12.377
r_dihedral_angle_3_deg11.835
r_dihedral_angle_1_deg5.384
r_mcangle_it3.123
r_scbond_it3.077
r_mcbond_it2.384
r_mcbond_other2.382
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.73
r_sphericity_free26.526
r_sphericity_bonded14.418
r_dihedral_angle_4_deg12.377
r_dihedral_angle_3_deg11.835
r_dihedral_angle_1_deg5.384
r_mcangle_it3.123
r_scbond_it3.077
r_mcbond_it2.384
r_mcbond_other2.382
r_angle_refined_deg1.186
r_angle_other_deg0.87
r_rigid_bond_restr0.814
r_chiral_restr0.066
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3381
Nucleic Acid Atoms
Solvent Atoms295
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling