8C56

CpG specific M.MpeI methyltransferase crystallized in the presence of 2'-deoxy-5-methylzebularine (5mZ) and 5-methylcytosine containing dsDNA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4DKJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.629410% PEG 3350, 150 mM NaCl, 50 mM sodium citrate (final pH, 5.6). For cryoprotection glycerol was added to 25% v/v
Crystal Properties
Matthews coefficientSolvent content
2.8156.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.259α = 90
b = 84.259β = 90
c = 173.883γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2013-02-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918409BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)CC (Half)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
12.42099.60.1140.1210.99916.898.62525153.298
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.54991.2031.2770.7032.058.8

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 REPLACEMENTTHROUGHOUT4DKJ2.419.8923997125399.560.175350.173260.21625RANDOM51.84
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]
0.580.58-1.16
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.755
r_dihedral_angle_4_deg14.394
r_dihedral_angle_3_deg14.346
r_dihedral_angle_1_deg5.523
r_long_range_B_refined3.77
r_long_range_B_other3.279
r_mcangle_it1.187
r_mcangle_other1.187
r_angle_refined_deg1.006
r_scangle_other0.951
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.755
r_dihedral_angle_4_deg14.394
r_dihedral_angle_3_deg14.346
r_dihedral_angle_1_deg5.523
r_long_range_B_refined3.77
r_long_range_B_other3.279
r_mcangle_it1.187
r_mcangle_other1.187
r_angle_refined_deg1.006
r_scangle_other0.951
r_angle_other_deg0.795
r_mcbond_it0.646
r_mcbond_other0.643
r_scbond_it0.52
r_scbond_other0.52
r_chiral_restr0.06
r_bond_refined_d0.009
r_gen_planes_refined0.003
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 Atoms3199
Nucleic Acid Atoms569
Solvent Atoms412
Heterogen Atoms33

Software

Software
Software NamePurpose
XDSdata reduction
XDSdata scaling
REFMACphasing
ARP/wARPmodel building
REFMACrefinement
PDB_EXTRACTdata extraction