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Crystal structure of the alkylsulfatase AtsK, a non-heme Fe(II) alphaketoglutarate dependent Dioxygenase in complex with 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 5.5 50 MM NA ACETATE 50 MM NA CITRATE PH 5.5, 10 % PEG 4000 30 % GLYCEROL
Crystal Properties Matthews coefficient Solvent content 3.17 60
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.447 α = 90 b = 144.876 β = 90 c = 160.692 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 2.07 38.92 98.8 0.1042 13.51 4.65 102501
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 2.07 2.2 94.6 0.4099 3.06 3.2
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1OIH 2.1 38.92 94338 4763 100 0.192 0.191 0.215 RANDOM 35.43
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] -1.97 2.51 -0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.294 r_scangle_it 5.989 r_scbond_it 3.745 r_mcangle_it 2.822 r_angle_refined_deg 1.601 r_mcbond_it 1.461 r_symmetry_vdw_refined 0.311 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.219 r_metal_ion_refined 0.204
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.294 r_scangle_it 5.989 r_scbond_it 3.745 r_mcangle_it 2.822 r_angle_refined_deg 1.601 r_mcbond_it 1.461 r_symmetry_vdw_refined 0.311 r_symmetry_hbond_refined 0.245 r_nbd_refined 0.219 r_metal_ion_refined 0.204 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.116 r_bond_refined_d 0.018 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 7708 Nucleic Acid Atoms Solvent Atoms 691 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling