5T64

X-ray structure of the C3-methyltransferase KijD1 from Actinomadura kijaniata in complex with TDP and SAH


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3NDI 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729320-23% PEG-3350, 100 mM MgCl2, 100 mM MOPS, 10 mM dTDP, 5 mM SAH
Crystal Properties
Matthews coefficientSolvent content
2.2244.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.34α = 90
b = 110.894β = 90
c = 143.251γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
11.787.69980.07510.74.289296
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)
11.71.892.40.3382.52.4

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 REPLACEMENTTHROUGHOUT3NDI1.73084825447198.30.182730.180720.22042RANDOM21.704
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]
-0.190.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.077
r_dihedral_angle_4_deg19.64
r_dihedral_angle_3_deg13.368
r_dihedral_angle_1_deg6.399
r_long_range_B_other6.15
r_long_range_B_refined6.146
r_scangle_other4.583
r_mcangle_it3.149
r_mcangle_other3.149
r_scbond_it3.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.077
r_dihedral_angle_4_deg19.64
r_dihedral_angle_3_deg13.368
r_dihedral_angle_1_deg6.399
r_long_range_B_other6.15
r_long_range_B_refined6.146
r_scangle_other4.583
r_mcangle_it3.149
r_mcangle_other3.149
r_scbond_it3.074
r_scbond_other3.062
r_mcbond_it2.258
r_mcbond_other2.257
r_angle_refined_deg1.712
r_angle_other_deg0.892
r_chiral_restr0.112
r_bond_refined_d0.01
r_gen_planes_refined0.008
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 Atoms6227
Nucleic Acid Atoms
Solvent Atoms687
Heterogen Atoms107

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing