4X7Y

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


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
2.3748.19

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.386α = 90
b = 89.926β = 90
c = 128.669γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-02-16MSINGLE 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
11.45085.512.96.599384

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 DIFFRACTIONTHROUGHOUT1.45094452492685.480.163250.16230.1814RANDOM19.271
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]
-0.991.65-0.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.767
r_dihedral_angle_4_deg14.347
r_dihedral_angle_3_deg11.549
r_long_range_B_refined5.827
r_dihedral_angle_1_deg5.754
r_long_range_B_other5.54
r_scangle_other1.705
r_angle_refined_deg1.24
r_scbond_it1.073
r_scbond_other1.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.767
r_dihedral_angle_4_deg14.347
r_dihedral_angle_3_deg11.549
r_long_range_B_refined5.827
r_dihedral_angle_1_deg5.754
r_long_range_B_other5.54
r_scangle_other1.705
r_angle_refined_deg1.24
r_scbond_it1.073
r_scbond_other1.073
r_mcangle_it1.051
r_mcangle_other1.051
r_angle_other_deg0.794
r_mcbond_it0.631
r_mcbond_other0.631
r_chiral_restr0.074
r_bond_refined_d0.006
r_gen_planes_refined0.006
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 Atoms3958
Nucleic Acid Atoms
Solvent Atoms496
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing