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MycF mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex with Mg, SAH and macrocin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4XVY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.1 20-30% PEG 5000 MME, 100 mM ammonium acetate and 100 mM BisTrisPropane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.4 48.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.229 α = 90 b = 91.642 β = 90 c = 128.427 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2012-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.033 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.75 50 97 0.085 13.6 7.3 60579
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 1.75 1.85 99.5 0.379 4.9 7.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4XVY 1.75 44.05 57489 3020 99.44 0.16617 0.16513 0.1771 0.18607 0.1963 RANDOM 17.523
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] -0.58 1.02 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.241 r_dihedral_angle_4_deg 16.016 r_dihedral_angle_3_deg 12.31 r_dihedral_angle_1_deg 5.872 r_long_range_B_refined 4.319 r_long_range_B_other 4.319 r_scangle_other 2.018 r_angle_refined_deg 1.347 r_scbond_it 1.24 r_scbond_other 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.241 r_dihedral_angle_4_deg 16.016 r_dihedral_angle_3_deg 12.31 r_dihedral_angle_1_deg 5.872 r_long_range_B_refined 4.319 r_long_range_B_other 4.319 r_scangle_other 2.018 r_angle_refined_deg 1.347 r_scbond_it 1.24 r_scbond_other 1.24 r_mcangle_it 1.088 r_mcangle_other 1.088 r_angle_other_deg 0.809 r_mcbond_it 0.665 r_mcbond_other 0.665 r_chiral_restr 0.076 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 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 3964 Nucleic Acid Atoms Solvent Atoms 399 Heterogen Atoms 180
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing