1TW3

Crystal structure of Carminomycin-4-O-methyltransferase (DnrK) in complex with S-adenosyl-L-homocystein (SAH) and 4-methoxy-e-rhodomycin T (M-ET)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherRdmB+SAM+DbrA complex

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6294ammonium sulphate, MES buffer, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
360

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 210.69α = 90
b = 53.134β = 105.03
c = 83.07γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I7111.09MAX III711

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
12.353594.80.07113.97417144171429
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)
2.352.41189.80.2145.5

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 REPLACEMENTTHROUGHOUTRdmB+SAM+DbrA complex2.353533956182995.610.195930.19330.24384RANDOM27.453
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]
-2.240.321.590.81
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.963
r_scangle_it2.511
r_scbond_it1.453
r_angle_refined_deg1.423
r_angle_other_deg1.024
r_mcangle_it0.914
r_mcbond_it0.465
r_symmetry_hbond_refined0.239
r_nbd_other0.233
r_symmetry_vdw_other0.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.963
r_scangle_it2.511
r_scbond_it1.453
r_angle_refined_deg1.423
r_angle_other_deg1.024
r_mcangle_it0.914
r_mcbond_it0.465
r_symmetry_hbond_refined0.239
r_nbd_other0.233
r_symmetry_vdw_other0.222
r_nbd_refined0.202
r_symmetry_vdw_refined0.184
r_xyhbond_nbd_refined0.176
r_chiral_restr0.105
r_nbtor_other0.087
r_bond_refined_d0.011
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5254
Nucleic Acid Atoms
Solvent Atoms350
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing