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Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ_V72I mutant in complex with 4-methoxycyclopeptin (1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5DAP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.16 43.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.78 α = 90 b = 120.91 β = 90 c = 66.76 γ = 90
Symmetry Space Group C 2 2 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 PIXEL DECTRIS EIGER X 16M 2016-10-15 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 1.55 50 98.9 0.04 17.2 3.8 42587
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 1.55 1.65 99.5 0.539
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 5DAP 1.55 15 40403 2127 98.72 0.14114 0.13924 0.1541 0.16804 0.1781 RANDOM 26.508
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] -1.21 1.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_sphericity_free 23.973 r_dihedral_angle_4_deg 16.051 r_dihedral_angle_3_deg 12.282 r_sphericity_bonded 6.557 r_dihedral_angle_1_deg 5.96 r_long_range_B_refined 2.866 r_long_range_B_other 2.513 r_mcangle_other 1.478 r_mcangle_it 1.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.961 r_sphericity_free 23.973 r_dihedral_angle_4_deg 16.051 r_dihedral_angle_3_deg 12.282 r_sphericity_bonded 6.557 r_dihedral_angle_1_deg 5.96 r_long_range_B_refined 2.866 r_long_range_B_other 2.513 r_mcangle_other 1.478 r_mcangle_it 1.477 r_scangle_other 1.464 r_rigid_bond_restr 1.384 r_scbond_it 1.324 r_scbond_other 1.319 r_angle_refined_deg 1.298 r_mcbond_it 1.138 r_mcbond_other 1.136 r_angle_other_deg 0.933 r_chiral_restr 0.074 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2228 Nucleic Acid Atoms Solvent Atoms 335 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing