4X7X

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5293.120-30% PEG 5000 MME, 100 mM ammonium acetate and 100 mM BisTrisPropane pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.448.8

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.229α = 90
b = 91.642β = 90
c = 128.427γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-11-15MSINGLE 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
11.7550970.08513.67.360579
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)
11.751.8599.50.3794.97.2

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 REPLACEMENTTHROUGHOUT4XVY1.7544.0557489302099.440.166170.165130.18607RANDOM17.523
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]
-0.581.02-0.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.241
r_dihedral_angle_4_deg16.016
r_dihedral_angle_3_deg12.31
r_dihedral_angle_1_deg5.872
r_long_range_B_refined4.319
r_long_range_B_other4.319
r_scangle_other2.018
r_angle_refined_deg1.347
r_scbond_it1.24
r_scbond_other1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.241
r_dihedral_angle_4_deg16.016
r_dihedral_angle_3_deg12.31
r_dihedral_angle_1_deg5.872
r_long_range_B_refined4.319
r_long_range_B_other4.319
r_scangle_other2.018
r_angle_refined_deg1.347
r_scbond_it1.24
r_scbond_other1.24
r_mcangle_it1.088
r_mcangle_other1.088
r_angle_other_deg0.809
r_mcbond_it0.665
r_mcbond_other0.665
r_chiral_restr0.076
r_bond_refined_d0.009
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 Atoms3964
Nucleic Acid Atoms
Solvent Atoms399
Heterogen Atoms180

Software

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