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Crystal structure of UbiX-like FMN prenyltransferase AF1214 from Archaeoglobus fulgidus, FMN complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 0.05 M Tris pH 8.5, 5 mM magnesium chloride, 50 mM potassium chloride, 5 mM ammonium sulfate, 30% (w/v) PEG400
cryoprotectant 5% PEG200
Crystal Properties Matthews coefficient Solvent content 1.91 35.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.56 α = 90 b = 98.56 β = 90 c = 98.56 γ = 90
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 2017-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.67 40.24 100 0.061 0.024 1 22.4 7.4 18632
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.67 1.71 100 1.38 0.55 0.563 1.4 7.2
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2EJB 1.67 40.237 1.34 18620 976 99.88 0.1494 0.1481 0.1736 0.153 RANDOM
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 21.544 f_angle_d 1.02 f_chiral_restr 0.073 f_bond_d 0.01 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1467 Nucleic Acid Atoms Solvent Atoms 199 Heterogen Atoms 36
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHENIX phasing PHENIX model building Coot model building