4X7Z

MycF mycinamicin III 3'-O-methyltransferase (E35Q, M56A, E139A variant) in complex with Mg, SAH and mycinamicin III (substrate)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.120-30% PEG 5000 MME, 100 mM ammonium acetate, 100 mM BisTrisPropane pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4249.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.354α = 90
b = 92.516β = 90
c = 127.798γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-03-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.033APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4474.949911.65.8107004
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)
11.441.5393.60.5611.43.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONTHROUGHOUT1.4446.85101687530998.970.153890.153180.16765RANDOM15.363
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]
-0.230.150.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.3
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg11.869
r_long_range_B_refined6.793
r_long_range_B_other6.792
r_dihedral_angle_1_deg5.936
r_scangle_other1.948
r_angle_refined_deg1.43
r_scbond_it1.238
r_scbond_other1.238
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.3
r_dihedral_angle_4_deg16.891
r_dihedral_angle_3_deg11.869
r_long_range_B_refined6.793
r_long_range_B_other6.792
r_dihedral_angle_1_deg5.936
r_scangle_other1.948
r_angle_refined_deg1.43
r_scbond_it1.238
r_scbond_other1.238
r_mcangle_it0.984
r_mcangle_other0.984
r_angle_other_deg0.841
r_mcbond_it0.61
r_mcbond_other0.61
r_chiral_restr0.085
r_bond_refined_d0.009
r_gen_planes_refined0.008
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3963
Nucleic Acid Atoms
Solvent Atoms779
Heterogen Atoms161

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing