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Crystal Structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase PlaO1 in complex with sodium succinate
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 36 % Tacsimate pH 7.0
soak: 15 min 375 mM Na succinate, 250 mM NaHCO3
Cryo: 100 % Tacsimate pH 7.0
Crystal Properties Matthews coefficient Solvent content 2.93 58.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.894 α = 90 b = 108.172 β = 93.87 c = 115.033 γ = 90
Symmetry Space Group P 1 21 1
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 2010-09-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 1.00000 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.55 78.72 99.8 0.039 0.046 0.024 1 19.4 3.8 226503 17.57
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 1.55 1.63 99.9 0.548 0.641 0.329 0.844 3.7
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 THROUGHOUT 1gqw 1.55 48.46 1.34 226398 11058 99.76 0.1516 0.1505 0.1511 0.1729 0.1729 27.7524
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]
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8943 Nucleic Acid Atoms Solvent Atoms 1067 Heterogen Atoms 77
Software Software Software Name Purpose PHENIX refinement autoPROC data reduction Aimless data scaling MOLREP phasing PDB_EXTRACT data extraction