4X7W

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4XVY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.120-30% PEG 5000 MME, 100 mM ammonium acetate, and 100 mM BisTrisPropane pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.4349.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.121α = 90
b = 92.528β = 90
c = 128.926γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-03-07MSINGLE 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)R Sym 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
11.4550930.119226.956748
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)
11.451.594.90.5914.26.1

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 REPLACEMENTTHROUGHOUT4XVY1.7532.8756748301497.580.174480.172640.20889RANDOM22.601
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]
-1.473.41-1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.065
r_dihedral_angle_4_deg18.074
r_dihedral_angle_3_deg12.943
r_dihedral_angle_1_deg6.258
r_long_range_B_other6.251
r_long_range_B_refined6.248
r_scangle_other3.856
r_scbond_it2.563
r_scbond_other2.562
r_angle_refined_deg2.017
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.065
r_dihedral_angle_4_deg18.074
r_dihedral_angle_3_deg12.943
r_dihedral_angle_1_deg6.258
r_long_range_B_other6.251
r_long_range_B_refined6.248
r_scangle_other3.856
r_scbond_it2.563
r_scbond_other2.562
r_angle_refined_deg2.017
r_mcangle_it1.855
r_mcangle_other1.854
r_mcbond_it1.368
r_mcbond_other1.367
r_angle_other_deg0.982
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
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 Atoms3964
Nucleic Acid Atoms
Solvent Atoms518
Heterogen Atoms148

Software

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