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Structural and Mechanistic Analysis of the Magnesium-Independent Aromatic Prenyltransferase CloQ from the Clorobiocin Biosynthetic Pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XLQ PDB ENTRY 2XLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 VAPOR DIFFUSION. PROTEIN AT 10 MG PER ML WAS MIXED WITH AN EQUAL VOLUME OF 3 M SODIUM FORMATE, 2 MM DITHIOTHREITOL IN 100 MM HEPES BUFFER AT PH 6.5
Crystal Properties Matthews coefficient Solvent content 3.12 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.57 α = 90 b = 135.57 β = 90 c = 95.7 γ = 90
Symmetry Space Group I 41 2 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 IMAGE PLATE MAR scanner 345 mm plate MIRRORS 2008-03-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
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 2.99 23.24 99.8 0.14 5.5 13.12 8365 -3 26.1
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 3.1 3.27 100 0.29 2.73 12.19
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 PDB ENTRY 2XLQ 3.1 23.24 7947 411 99.98 0.1815 0.17864 0.1827 0.23586 0.2393 RANDOM 18.9
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] -1.36 -1.36 2.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.855 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 19.417 r_dihedral_angle_1_deg 6.807 r_scangle_it 2.633 r_angle_refined_deg 1.488 r_scbond_it 1.446 r_mcangle_it 1.073 r_angle_other_deg 0.92 r_mcbond_it 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.855 r_dihedral_angle_4_deg 19.763 r_dihedral_angle_3_deg 19.417 r_dihedral_angle_1_deg 6.807 r_scangle_it 2.633 r_angle_refined_deg 1.488 r_scbond_it 1.446 r_mcangle_it 1.073 r_angle_other_deg 0.92 r_mcbond_it 0.54 r_chiral_restr 0.078 r_mcbond_other 0.064 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2369 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing