5T6B

X-ray structure of the KijD1 C3-methyltransfeerase, converted to monomeric form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5T64 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929318-22% PEG-3350, 2%MPD, 100 mM MES, 10 mM TDP, 5 mM SAH
Crystal Properties
Matthews coefficientSolvent content
1.9436.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.707α = 96.05
b = 82.455β = 110.7
c = 82.825γ = 112.09
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDBruker Platinum 1352015-12-12MSINGLE 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
127596.60.0747.33.190291
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)
122.1910.3052.11.8

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 REPLACEMENTTHROUGHOUT5T6423085763452896.60.178550.175560.23424RANDOM25.19
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]
-0.72-0.110.090.450.6-0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.969
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg15.553
r_dihedral_angle_1_deg6.659
r_long_range_B_refined5.44
r_long_range_B_other5.439
r_scangle_other3.817
r_mcangle_it2.961
r_mcangle_other2.961
r_scbond_it2.389
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.969
r_dihedral_angle_4_deg18.325
r_dihedral_angle_3_deg15.553
r_dihedral_angle_1_deg6.659
r_long_range_B_refined5.44
r_long_range_B_other5.439
r_scangle_other3.817
r_mcangle_it2.961
r_mcangle_other2.961
r_scbond_it2.389
r_scbond_other2.368
r_mcbond_it1.879
r_mcbond_other1.879
r_angle_refined_deg1.773
r_angle_other_deg1.038
r_chiral_restr0.099
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms12428
Nucleic Acid Atoms
Solvent Atoms737
Heterogen Atoms216

Software

Software
Software NamePurpose
REFMACrefinement
SAINTdata reduction
SADABSdata scaling
PHASERphasing