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Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GQW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 310 Anaerobically:
60 % Tacsimate pH 7.0, 10 mM Imidazole, 30 mM NaCl, 1.5 mM Fe(II)SO4, 1.5 mM alpha-ketoglutarate, 1.5 mM ascorbate, 2.5 mM PL-CD6 (substrate)
Cryo-protechtion: 10 % (2R,3R)-butane-2,3-diol
Crystal Properties Matthews coefficient Solvent content 3.03 59.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 117.923 α = 90 b = 108.229 β = 90 c = 65.373 γ = 90
Symmetry Space Group P 21 21 2
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 MARMOSAIC 225 mm CCD 2009-08-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.00630 SLS X06DA
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 2.695 79.74 98.2 0.11 18.4 14.2 23401
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 2.7 2.84 100 1.022 14.9
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 1GQW 2.695 79.74 23225 1166 97.6 0.242 0.2397 0.2356 0.287 0.2762 RANDOM 71.47
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] -9.7423 7.8724 1.8699
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 18.34 t_omega_torsion 3.02 t_angle_deg 0.94 t_bond_d 0.008 t_dihedral_angle_d t_gen_planes t_it t_chiral_improper_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4050 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 12
Software Software Software Name Purpose BUSTER refinement autoPROC data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction