1TW2

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 DROP8.5294PEG4000, sodium acetate, Tris-buffer, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.654

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.682α = 90
b = 102.582β = 90
c = 124.256γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-11-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.98ESRFID29

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
12.579.0699.90.10412.48.9275692756931
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)
2.52.56599.90.3224.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTRdmB+SAM+DbrA complex2.5542615626156138799.930.20640.20640.202960.27052RANDOM25.953
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]
-1.59-1.132.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.744
r_scangle_it2.25
r_angle_refined_deg1.531
r_scbond_it1.311
r_angle_other_deg1.001
r_mcangle_it0.939
r_mcbond_it0.495
r_symmetry_vdw_other0.3
r_nbd_other0.231
r_nbd_refined0.215
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.744
r_scangle_it2.25
r_angle_refined_deg1.531
r_scbond_it1.311
r_angle_other_deg1.001
r_mcangle_it0.939
r_mcbond_it0.495
r_symmetry_vdw_other0.3
r_nbd_other0.231
r_nbd_refined0.215
r_symmetry_vdw_refined0.215
r_xyhbond_nbd_refined0.199
r_symmetry_hbond_refined0.103
r_chiral_restr0.092
r_nbtor_other0.088
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_gen_planes_other0.004
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5309
Nucleic Acid Atoms
Solvent Atoms165
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing