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Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ in complex with 4-Methoxycyclopeptin
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, SITTING DROP 8 293 100 mM TRIS/HCl, 1 M LiBr, 27% PEG 6000
Crystal Properties Matthews coefficient Solvent content 2.15 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.73 α = 90 b = 120.01 β = 90 c = 67.02 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 PSI PILATUS 6M 2015-03-07 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 1.7 30 98.1 0.057 14.4 4.4 32625 32005
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 1.7 1.8 98.8 0.563 2.8
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 1.7 15 30403 1601 98.05 0.1764 0.17519 0.1894 0.19674 0.2094 RANDOM 29.326
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] -2.18 3.74 -1.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.816 r_sphericity_free 26.27 r_dihedral_angle_4_deg 18.903 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_1_deg 5.719 r_sphericity_bonded 4.931 r_long_range_B_refined 2.9 r_long_range_B_other 2.398 r_rigid_bond_restr 1.604 r_mcangle_other 1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.816 r_sphericity_free 26.27 r_dihedral_angle_4_deg 18.903 r_dihedral_angle_3_deg 15.237 r_dihedral_angle_1_deg 5.719 r_sphericity_bonded 4.931 r_long_range_B_refined 2.9 r_long_range_B_other 2.398 r_rigid_bond_restr 1.604 r_mcangle_other 1.54 r_mcangle_it 1.539 r_scangle_other 1.432 r_scbond_it 1.302 r_scbond_other 1.301 r_mcbond_it 1.251 r_mcbond_other 1.25 r_angle_refined_deg 1.19 r_angle_other_deg 0.799 r_chiral_restr 0.071 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 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 2227 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 34
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing