6QSR

The Dehydratase Heterocomplex ApeI:P from Xenorhabdus doucetiae


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72930.1 M HEPES, 30% PEG 6000
Crystal Properties
Matthews coefficientSolvent content
2.0841.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 144.68α = 90
b = 47.77β = 104.65
c = 42.68γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2018-05-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.853095.90.06911323313
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)
11.851.9597.60.472.7

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 REPLACEMENTTHROUGHOUT3ESI1.851522103116395.830.202120.199230.23804RANDOM30.667
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]
-0.1-0.360.47-0.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.447
r_sphericity_free22.227
r_dihedral_angle_4_deg19.301
r_dihedral_angle_3_deg15.119
r_dihedral_angle_1_deg5.933
r_sphericity_bonded4.305
r_long_range_B_refined2.587
r_long_range_B_other2.484
r_scbond_it1.866
r_scbond_other1.865
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.447
r_sphericity_free22.227
r_dihedral_angle_4_deg19.301
r_dihedral_angle_3_deg15.119
r_dihedral_angle_1_deg5.933
r_sphericity_bonded4.305
r_long_range_B_refined2.587
r_long_range_B_other2.484
r_scbond_it1.866
r_scbond_other1.865
r_scangle_other1.667
r_mcangle_it1.505
r_mcangle_other1.505
r_mcbond_it1.392
r_mcbond_other1.39
r_angle_refined_deg1.294
r_rigid_bond_restr1.053
r_angle_other_deg0.884
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.005
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2127
Nucleic Acid Atoms
Solvent Atoms105
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing