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Crystal structure of PieE, the flavin-dependent monooxygenase involved in the biosynthesis of piericidin A1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4Z2U
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH 7.5 295 30% PEG 400, 0.2M MgCl2, and 0.1 HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.68 54.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.569 α = 90 b = 187.409 β = 90 c = 241.279 γ = 90
Symmetry Space Group P 21 21 21
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 MAR CCD 130 mm 2016-01-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.9795 CLSI 08ID-1
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 2.02 49.34 99.8 0.109 0.122 0.054 0.994 8.8 4.7 270573
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 2.02 2.05 100 0.803 0.906 0.41 0.689 4.5
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 4Z2U 2.02 49.34 257001 13453 99.77 0.1716 0.1698 0.1789 0.204 0.21 RANDOM 34.364
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] 1.98 -0.57 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.542 r_dihedral_angle_4_deg 21.12 r_dihedral_angle_3_deg 14.718 r_dihedral_angle_1_deg 6.878 r_angle_refined_deg 1.75 r_angle_other_deg 1.431 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.542 r_dihedral_angle_4_deg 21.12 r_dihedral_angle_3_deg 14.718 r_dihedral_angle_1_deg 6.878 r_angle_refined_deg 1.75 r_angle_other_deg 1.431 r_chiral_restr 0.083 r_bond_refined_d 0.011 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 26592 Nucleic Acid Atoms Solvent Atoms 2342 Heterogen Atoms 646
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MOLREP phasing