4XVY

MycF mycinamicin III 3'-O-methyltransferase in complex with SAH


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION293.120-30% PEG 3350, 100 mM BisTrisPropane pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.3347.21

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.057α = 90
b = 89.892β = 90
c = 127.655γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2009-03-11MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D1.0332APS23-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
12.443.7398.40.11415.16.422837

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 REPLACEMENTTHROUGHOUT4XVZ2.4243.7321163114297.680.208890.206260.25807RANDOM60.565
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]
-1.787.49-5.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.331
r_dihedral_angle_4_deg17.474
r_dihedral_angle_3_deg17.18
r_long_range_B_refined6.255
r_long_range_B_other6.255
r_dihedral_angle_1_deg5.881
r_scangle_other2.669
r_mcangle_it2.408
r_mcangle_other2.407
r_scbond_it1.609
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.331
r_dihedral_angle_4_deg17.474
r_dihedral_angle_3_deg17.18
r_long_range_B_refined6.255
r_long_range_B_other6.255
r_dihedral_angle_1_deg5.881
r_scangle_other2.669
r_mcangle_it2.408
r_mcangle_other2.407
r_scbond_it1.609
r_scbond_other1.608
r_angle_refined_deg1.539
r_mcbond_it1.429
r_mcbond_other1.429
r_angle_other_deg0.998
r_chiral_restr0.084
r_bond_refined_d0.013
r_gen_planes_refined0.007
r_bond_other_d0.004
r_gen_planes_other0.004
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 Atoms3940
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
DENZOdata reduction
PHASERphasing