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Crystal structure of the Y135A mutant of DIMT1 in complex with adenosylornithine (SFG) 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 2.55 51.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.06 α = 90 b = 79.96 β = 116.28 c = 85.41 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 2022-10-07 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 2.6 76.58 94.3 0.19 0.218 0.104 0.939 5.8 4.4 20945
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 2.6 2.72 82.1 0.566 0.643 0.3 0.846 4.4
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 2.6 76.58 19804 1058 93.75 0.26369 0.26232 0.2682 0.28909 0.2916 RANDOM 52.758
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] 1.88 2.19 -1.9 -1.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.301 r_dihedral_angle_1_deg 8.411 r_dihedral_angle_2_deg 7.634 r_long_range_B_refined 6.333 r_long_range_B_other 6.333 r_mcangle_other 3.664 r_mcangle_it 3.659 r_scangle_other 3.103 r_mcbond_it 2.21 r_mcbond_other 2.183
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 18.301 r_dihedral_angle_1_deg 8.411 r_dihedral_angle_2_deg 7.634 r_long_range_B_refined 6.333 r_long_range_B_other 6.333 r_mcangle_other 3.664 r_mcangle_it 3.659 r_scangle_other 3.103 r_mcbond_it 2.21 r_mcbond_other 2.183 r_scbond_it 1.881 r_scbond_other 1.879 r_angle_refined_deg 1.567 r_angle_other_deg 0.518 r_chiral_restr 0.07 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 4376 Nucleic Acid Atoms Solvent Atoms 102 Heterogen Atoms 58
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