5A60

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


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
120% PEG 3,350, 0.2 M NACL
Crystal Properties
Matthews coefficientSolvent content
3.0159.18

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 89.924α = 90
b = 89.924β = 90
c = 125.577γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100DECTRIS HYBRID PHOTON2014-03-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.8248.8898.80.0714.919.750673-3
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)
11.821.9396.90.942.189.06

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 DIFFRACTIONSADTHROUGHOUTNONE1.8248.8847520251897.680.152530.150530.18948RANDOM55.658
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]
-0.56-0.28-0.561.82
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.36
r_sphericity_free34.338
r_sphericity_bonded18.983
r_dihedral_angle_4_deg13.438
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg5.42
r_mcangle_it4.248
r_scbond_it3.792
r_mcbond_other3.077
r_mcbond_it3.076
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.36
r_sphericity_free34.338
r_sphericity_bonded18.983
r_dihedral_angle_4_deg13.438
r_dihedral_angle_3_deg12.34
r_dihedral_angle_1_deg5.42
r_mcangle_it4.248
r_scbond_it3.792
r_mcbond_other3.077
r_mcbond_it3.076
r_rigid_bond_restr1.193
r_angle_refined_deg1.149
r_angle_other_deg0.87
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
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 Atoms3385
Nucleic Acid Atoms
Solvent Atoms289
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
SHARPphasing
RESOLVEphasing
PHENIXphasing