6EXD

Crystal structure of DotM cytoplasmic domain (residues 153-380) SeMet derivative


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2890.1 M MES pH 6.0 0.15 M NH4SO4 25 % w/v PEG 4000
Crystal Properties
Matthews coefficientSolvent content
2.5251.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118α = 90
b = 118β = 90
c = 66.4γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-12-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 10.979SOLEILPROXIMA 1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)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
12.1450.0199.50.2530.979.1113.229190
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.162.2299.21.1370.4151.512.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.1450.0127700146999.540.193030.19130.22749RANDOM31.303
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]
0.810.410.81-2.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_dihedral_angle_4_deg22.206
r_dihedral_angle_3_deg18.459
r_long_range_B_refined8.5
r_long_range_B_other8.49
r_dihedral_angle_1_deg6.824
r_scangle_other6.406
r_mcangle_it4.361
r_mcangle_other4.361
r_scbond_it4.114
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.372
r_dihedral_angle_4_deg22.206
r_dihedral_angle_3_deg18.459
r_long_range_B_refined8.5
r_long_range_B_other8.49
r_dihedral_angle_1_deg6.824
r_scangle_other6.406
r_mcangle_it4.361
r_mcangle_other4.361
r_scbond_it4.114
r_scbond_other4.107
r_mcbond_it2.72
r_mcbond_other2.718
r_angle_refined_deg2.084
r_angle_other_deg1.158
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.01
r_bond_other_d0.003
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 Atoms3496
Nucleic Acid Atoms
Solvent Atoms131
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
BUCCANEERphasing