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Fe(II)/(alpha)ketoglutarate-dependent dioxygenase AsqJ
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NAO
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 2.13 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.11 α = 90 b = 117.71 β = 90 c = 67.16 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 97.5 0.056 16.2 5.4 32252 31446
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 97.9 0.511 3.6
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 4NAO 1.7 15 29873 1573 97.47 0.19244 0.17948 0.1963 0.1954 0.2134 RANDOM 27.536
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] -1.74 3.19 -1.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.302 r_sphericity_free 24.235 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_3_deg 14.96 r_dihedral_angle_1_deg 5.78 r_sphericity_bonded 4.676 r_long_range_B_refined 2.548 r_long_range_B_other 2.104 r_mcangle_it 1.274 r_mcangle_other 1.274
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.302 r_sphericity_free 24.235 r_dihedral_angle_4_deg 17.934 r_dihedral_angle_3_deg 14.96 r_dihedral_angle_1_deg 5.78 r_sphericity_bonded 4.676 r_long_range_B_refined 2.548 r_long_range_B_other 2.104 r_mcangle_it 1.274 r_mcangle_other 1.274 r_scbond_it 1.272 r_scbond_other 1.272 r_scangle_other 1.2 r_angle_refined_deg 1.091 r_mcbond_it 1.074 r_mcbond_other 1.073 r_rigid_bond_restr 1 r_angle_other_deg 0.749 r_chiral_restr 0.064 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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 273 Heterogen Atoms 11
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing