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A nonheme iron- and alpha-ketoglutarate- dependent halogenase that catalyzes nucleotide substrates
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7W5S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 Ammonium Sulfate, HEPES pH 7.5, PEG 400, di-Potassium hydrogen phosphate
Crystal Properties Matthews coefficient Solvent content 2.25 45.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.649 α = 90 b = 71.255 β = 90 c = 82.473 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 CMOS BRUKER PHOTON 100 2020-12-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 LIQUID ANODE BRUKER METALJET 1.34138
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 1.74 32.71 99.2 0.06 24.2 11.4 32596
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 1.74 1.77 0.262
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 7W5S 1.74 32.71 30623 1601 99.03 0.1595 0.1579 0.1718 0.189 0.202 RANDOM 18.359
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] -4.61 -5 9.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.933 r_dihedral_angle_4_deg 18.704 r_dihedral_angle_3_deg 13.346 r_dihedral_angle_1_deg 6.496 r_angle_refined_deg 1.814 r_angle_other_deg 1.523 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.933 r_dihedral_angle_4_deg 18.704 r_dihedral_angle_3_deg 13.346 r_dihedral_angle_1_deg 6.496 r_angle_refined_deg 1.814 r_angle_other_deg 1.523 r_chiral_restr 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2211 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 36
Software Software Software Name Purpose SADABS data scaling REFMAC refinement PDB_EXTRACT data extraction SAINT data reduction PHENIX phasing