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O-Methyltransferase Plu4895 in complex with SAH and AQ-256
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8BIG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.2 M Ammonium iodide, 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.13 42.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.06 α = 90 b = 40.13 β = 92.47 c = 119.29 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 PIXEL DECTRIS EIGER X 16M 2020-11-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.0 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 46 97.8 0.084 9.9 3.3 25372
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 98.3 0.683 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 8BIG 2.4 30 24089 1268 97.72 0.26697 0.26523 0.30113 0.3063 RANDOM 65.207
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] -2.31 -1.47 3.84 -1.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.694 r_dihedral_angle_3_deg 16.99 r_dihedral_angle_4_deg 16.341 r_dihedral_angle_1_deg 5.97 r_long_range_B_refined 3.44 r_long_range_B_other 3.44 r_mcangle_it 1.418 r_mcangle_other 1.418 r_angle_refined_deg 1.182 r_angle_other_deg 1.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.694 r_dihedral_angle_3_deg 16.99 r_dihedral_angle_4_deg 16.341 r_dihedral_angle_1_deg 5.97 r_long_range_B_refined 3.44 r_long_range_B_other 3.44 r_mcangle_it 1.418 r_mcangle_other 1.418 r_angle_refined_deg 1.182 r_angle_other_deg 1.066 r_scangle_other 0.812 r_mcbond_it 0.766 r_mcbond_other 0.766 r_scbond_it 0.415 r_scbond_other 0.415 r_chiral_restr 0.039 r_gen_planes_refined 0.003 r_bond_refined_d 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 5140 Nucleic Acid Atoms Solvent Atoms 34 Heterogen Atoms 104
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing