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MycF mycinamicin III 3'-O-methyltransferase (E35Q, E139A variant) in complex with Mg, SAH and mycinamicin VI (MycE substrate)
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 293.1 20-30% PEG 5000 MME, 100 mM ammonium acetate, and 100 mM BisTrisPropane pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.43 49.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 50.121 α = 90 b = 92.528 β = 90 c = 128.926 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 2013-03-07 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 1.45 50 93 0.119 22 6.9 56748
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 1.45 1.5 94.9 0.591 4.2 6.1
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 32.87 56748 3014 97.58 0.17448 0.17264 0.1852 0.20889 0.2181 RANDOM 22.601
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] -1.47 3.41 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.065 r_dihedral_angle_4_deg 18.074 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 6.258 r_long_range_B_other 6.251 r_long_range_B_refined 6.248 r_scangle_other 3.856 r_scbond_it 2.563 r_scbond_other 2.562 r_angle_refined_deg 2.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.065 r_dihedral_angle_4_deg 18.074 r_dihedral_angle_3_deg 12.943 r_dihedral_angle_1_deg 6.258 r_long_range_B_other 6.251 r_long_range_B_refined 6.248 r_scangle_other 3.856 r_scbond_it 2.563 r_scbond_other 2.562 r_angle_refined_deg 2.017 r_mcangle_it 1.855 r_mcangle_other 1.854 r_mcbond_it 1.368 r_mcbond_other 1.367 r_angle_other_deg 0.982 r_chiral_restr 0.129 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_gen_planes_other 0.002 r_bond_other_d 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 518 Heterogen Atoms 148
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing