6IYR | pdb_00006iyr

Crystal Structure of the acyltransferase domain from module 8 of the salinomycin polyketide synthase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2HG4 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION8.22930.056M NaH2PO4, 1.544M K2HPO4 pH 8.2
Crystal Properties
Matthews coefficientSolvent content
3.0459.58

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 123.244α = 90
b = 123.244β = 90
c = 78.532γ = 90
Symmetry
Space GroupP 42 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2016-05-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97914SSRFBL17U1

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
12.055099.930.08756.414.536404
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)
12.052.0999.680.665.314.6

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2HG42.055036404190199.930.203160.201140.210.241660.25RANDOM37.968
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]
-0.43-0.430.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.404
r_dihedral_angle_4_deg24.648
r_dihedral_angle_3_deg21.55
r_long_range_B_other10.463
r_long_range_B_refined10.446
r_scangle_other9.793
r_scbond_it7.47
r_scbond_other7.328
r_dihedral_angle_1_deg7.202
r_mcangle_other5.042
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.404
r_dihedral_angle_4_deg24.648
r_dihedral_angle_3_deg21.55
r_long_range_B_other10.463
r_long_range_B_refined10.446
r_scangle_other9.793
r_scbond_it7.47
r_scbond_other7.328
r_dihedral_angle_1_deg7.202
r_mcangle_other5.042
r_mcangle_it5.041
r_mcbond_it4.49
r_mcbond_other4.486
r_angle_refined_deg1.516
r_angle_other_deg0.792
r_chiral_restr0.121
r_gen_planes_refined0.016
r_bond_refined_d0.012
r_gen_planes_other0.001
r_bond_other_d
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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3098
Nucleic Acid Atoms
Solvent Atoms88
Heterogen Atoms5

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing