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Crystal structure of AlkB in complex with manganese and N-(4-((6-((carboxymethyl)carbamoyl)-5-hydroxypyridin-2-yl)amino)phenyl)-N-oxohydroxylammonium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1M HEPES pH 7.5, 2mM MnCl2, 0.1M NaCl, 22% w/v PEG 3350, AlkB protein 20mg/ml, 2mM N-(4-((6-((carboxymethyl)carbamoyl)-5-hydroxypyridin-2-yl)amino)phenyl)-N-oxohydroxylammonium, 0.5% v/v DMSO
Crystal Properties Matthews coefficient Solvent content 2.09 41.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.88 α = 77.6 b = 38.75 β = 75.38 c = 40.25 γ = 66.14
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 DECTRIS PILATUS 6M-F K-B mirrors 2019-12-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 1.25 35.15 92.9 0.051 0.9935 20.48 3.3 50272 13.08
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.25 1.27 90.82 0.0754 0.091 0.05 0.9906 12.16 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2FDJ 1.25 35.15 2.09 50268 2427 92.92 0.1471 0.1463 0.1465 0.1639 0.1632 18.88
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.8551 f_angle_d 1.2043 f_chiral_restr 0.0895 f_plane_restr 0.0169 f_bond_d 0.0117
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1563 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 25
Software Software Software Name Purpose PHENIX refinement xia2 data reduction Aimless data scaling PHASER phasing