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Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase in complex with iron and alphaketoglutarate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OIH PDB ENTRY 1OIH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 50 MM NA SULFATE, 50 MM NA CITRATE PH 5.5, 10% PEG 4000, 30% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.18 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.421 α = 90 b = 147.329 β = 90 c = 158.573 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 MARRESEARCH PREMIRROR, TRIANGULAR MONOCHROMATOR, BENT MIRROR M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.19 20 97.5 0.0644 19.96 6.38 86268
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 2.19 2.3 83.1 0.452 5.1 5.61
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OIH 2.19 20 81913 4246 97.7 0.197 0.195 0.1972 0.22 RANDOM 33.95
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] -2.27 1.71 0.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.603 r_scangle_it 5.589 r_scbond_it 3.688 r_mcangle_it 2.863 r_angle_refined_deg 1.635 r_mcbond_it 1.54 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.603 r_scangle_it 5.589 r_scbond_it 3.688 r_mcangle_it 2.863 r_angle_refined_deg 1.635 r_mcbond_it 1.54 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.208 r_symmetry_hbond_refined 0.2 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.119 r_metal_ion_refined 0.058 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7594 Nucleic Acid Atoms Solvent Atoms 573 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling