4X7U

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


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
2.3647.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.856α = 90
b = 90.85β = 90
c = 128.641γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2012-04-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B1.033APS23-ID-B

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
11.655099.40.07312.63.671066
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.651.6899.30.5882.13.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4XVY1.6543.7167012357199.320.148860.147860.16788RANDOM18.255
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]
-0.421.41-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.907
r_dihedral_angle_4_deg17.543
r_dihedral_angle_3_deg12.458
r_long_range_B_refined6.114
r_dihedral_angle_1_deg5.838
r_long_range_B_other5.505
r_scangle_other1.843
r_angle_refined_deg1.28
r_mcangle_it1.125
r_mcangle_other1.125
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.907
r_dihedral_angle_4_deg17.543
r_dihedral_angle_3_deg12.458
r_long_range_B_refined6.114
r_dihedral_angle_1_deg5.838
r_long_range_B_other5.505
r_scangle_other1.843
r_angle_refined_deg1.28
r_mcangle_it1.125
r_mcangle_other1.125
r_scbond_it1.106
r_scbond_other1.106
r_angle_other_deg0.804
r_mcbond_it0.66
r_mcbond_other0.66
r_chiral_restr0.074
r_bond_refined_d0.007
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 Atoms3996
Nucleic Acid Atoms
Solvent Atoms572
Heterogen Atoms150

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing