8X4O

Crystal structure of the Y135A mutant of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8X3W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH6.52930.2 M Zinc Acetate Dihydrate, 0.1 M Sodium Cacodylate Trihydrate pH 6.5, 18% (w/v) PEG 8000
Crystal Properties
Matthews coefficientSolvent content
2.3647.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 125.539α = 90
b = 125.539β = 90
c = 37.14γ = 120
Symmetry
Space GroupP 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++VariMax HF2022-10-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim 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
1362.8594.90.0980.1070.0440.9959.86.112475
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.181000.4540.4970.2010.9156.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT362.851149697194.890.226090.219490.30437RANDOM113.586
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]
1.650.821.65-5.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.675
r_long_range_B_refined10.481
r_long_range_B_other10.48
r_dihedral_angle_2_deg8.672
r_dihedral_angle_1_deg8.356
r_mcangle_it6.095
r_mcangle_other6.094
r_scangle_other6.05
r_mcbond_it3.691
r_mcbond_other3.688
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.675
r_long_range_B_refined10.481
r_long_range_B_other10.48
r_dihedral_angle_2_deg8.672
r_dihedral_angle_1_deg8.356
r_mcangle_it6.095
r_mcangle_other6.094
r_scangle_other6.05
r_mcbond_it3.691
r_mcbond_other3.688
r_scbond_it3.613
r_scbond_other3.612
r_angle_refined_deg1.134
r_angle_other_deg0.826
r_chiral_restr0.054
r_bond_other_d0.024
r_bond_refined_d0.012
r_gen_planes_other0.007
r_gen_planes_refined0.005
r_dihedral_angle_4_deg
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 Atoms4364
Nucleic Acid Atoms
Solvent Atoms21
Heterogen Atoms50

Software

Software
Software NamePurpose
HKL-3000data collection
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Cootmodel building
PDB_EXTRACTdata extraction