4AX8

Medium resolution structure of the bifunctional kinase- methyltransferase WbdD


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.26 M LITHIUM SULFATE, 0.1 M TRIS-HCL PH 8.4, 1.12 M AMMONIUM SULFATE, 5 MM SAM/MG/ATP
Crystal Properties
Matthews coefficientSolvent content
3.161

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 167.34α = 90
b = 167.34β = 90
c = 167.34γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMONDDiamond

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.83099.50.120.110.3191851
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.8597.51.1

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 DIFFRACTIONSADTHROUGHOUTNONE368.321493678499.620.213450.212440.23282RANDOM60.475
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.292
r_dihedral_angle_4_deg19.561
r_dihedral_angle_3_deg15.995
r_dihedral_angle_1_deg6.494
r_angle_other_deg2.766
r_angle_refined_deg1.837
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.292
r_dihedral_angle_4_deg19.561
r_dihedral_angle_3_deg15.995
r_dihedral_angle_1_deg6.494
r_angle_other_deg2.766
r_angle_refined_deg1.837
r_chiral_restr0.098
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.005
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3646
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement