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Crystal Structure of AlkB in complex with Fe(III) and N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3T4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 25% PEG 3350, 0.2M ammonium sulfate, 0.1M tris-hydrochloride pH8.5, 2.2mM ammonium iron(II) sulfate, 1mM N-Oxalyl-S-(2-napthalenemethyl)-L-cysteine, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.07 α = 76.33 b = 39.234 β = 74.56 c = 40.261 γ = 65.28
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 RIGAKU SATURN 944+ osmic HF 2011-04-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5412
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 50 93.2 0.107 23.4 4.4 22000 20297 1 20.07
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 1.76 81.2 0.282 2.852 1.9 1776
Refinement Statistics Diffraction ID Structure Solution 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT 3T4H 1.732 22.994 1.97 19227 1889 94.06 0.1649 0.1608 0.1582 0.2019 0.1982 random 27.7213
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] -1.8522 2.5271 -2.4013 -0.3767 -5.2169 2.2289
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.023 f_angle_d 1.486 f_chiral_restr 0.112 f_bond_d 0.011 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1544 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PHENIX refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling