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Crystal structure of DIMT1 in complex with 5'-methylthioadenosine from Pyrococcus horikoshii (FormII)
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 VAPOR DIFFUSION, HANGING DROP 6.4 293 0.2 M Zinc Acetate Dihydrate, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.6 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.74 α = 90 b = 80.23 β = 116.17 c = 85.71 γ = 90
Symmetry Space Group C 1 2 1
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 2022-05-23 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 2.5 76.92 95.2 0.131 0.152 0.075 0.987 7.1 4.1 24312
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 2.5 2.6 100 0.704 0.808 0.39 0.778 4.1
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 2.5 76.92 23099 1178 95.05 0.23364 0.23109 0.2376 0.28213 0.2832 RANDOM 48.118
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] 2.75 -0.27 -1.5 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.431 r_dihedral_angle_2_deg 8.431 r_dihedral_angle_1_deg 7.919 r_long_range_B_other 7.622 r_long_range_B_refined 7.613 r_scangle_other 4.996 r_mcangle_other 4.215 r_mcangle_it 4.211 r_scbond_it 3.148 r_scbond_other 3.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.431 r_dihedral_angle_2_deg 8.431 r_dihedral_angle_1_deg 7.919 r_long_range_B_other 7.622 r_long_range_B_refined 7.613 r_scangle_other 4.996 r_mcangle_other 4.215 r_mcangle_it 4.211 r_scbond_it 3.148 r_scbond_other 3.148 r_mcbond_it 2.685 r_mcbond_other 2.685 r_angle_refined_deg 1.546 r_angle_other_deg 0.509 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.004 r_gen_planes_other 0.001 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 4384 Nucleic Acid Atoms Solvent Atoms 152 Heterogen Atoms 109
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