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Crystal structure of the Y135A mutant of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8X3W
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 6.5 293 0.2 M Zinc Acetate Dihydrate, 0.1 M Sodium Cacodylate Trihydrate pH 6.5, 18% (w/v) PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.36 47.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.539 α = 90 b = 125.539 β = 90 c = 37.14 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE RIGAKU RAXIS IV++ VariMax HF 2022-10-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3 62.85 94.9 0.098 0.107 0.044 0.995 9.8 6.1 12475
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) Redundancy Number Unique Reflections (All) 1 3 3.18 100 0.454 0.497 0.201 0.915 6.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3 62.85 11496 971 94.89 0.22609 0.21949 0.2205 0.30437 0.2989 RANDOM 113.586
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] 1.65 0.82 1.65 -5.35
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.675 r_long_range_B_refined 10.481 r_long_range_B_other 10.48 r_dihedral_angle_2_deg 8.672 r_dihedral_angle_1_deg 8.356 r_mcangle_it 6.095 r_mcangle_other 6.094 r_scangle_other 6.05 r_mcbond_it 3.691 r_mcbond_other 3.688
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.675 r_long_range_B_refined 10.481 r_long_range_B_other 10.48 r_dihedral_angle_2_deg 8.672 r_dihedral_angle_1_deg 8.356 r_mcangle_it 6.095 r_mcangle_other 6.094 r_scangle_other 6.05 r_mcbond_it 3.691 r_mcbond_other 3.688 r_scbond_it 3.613 r_scbond_other 3.612 r_angle_refined_deg 1.134 r_angle_other_deg 0.826 r_chiral_restr 0.054 r_bond_other_d 0.024 r_bond_refined_d 0.012 r_gen_planes_other 0.007 r_gen_planes_refined 0.005 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 Atoms Number Protein Atoms 4364 Nucleic Acid Atoms Solvent Atoms 21 Heterogen Atoms 50
Software Software Software Name Purpose HKL-3000 data collection MOSFLM data reduction Aimless data scaling PHASER phasing REFMAC refinement Coot model building PDB_EXTRACT data extraction