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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 (10 MG/ML) MIXED WITH AN EQUAL VOLUME OF 3 M SODIUM FORMATE, 2 MM DITHIOTHREITOL,100 MM HEPES PH (6.5).
Crystal Properties Matthews coefficient Solvent content 3.12 60.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.34 α = 90 b = 135.34 β = 90 c = 98.64 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 CCD ADSC CCD 2008-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 Diamond I02
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 2.22 51.57 100 0.1 5.83 7.45 23029 -3 36.7
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 2.22 2.34 100 0.62 1.22 6.91
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 2.22 43.85 21654 1169 99.1 0.17572 0.17386 0.174 0.20959 0.2021 RANDOM 25.787
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] -0.69 -0.69 1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.263 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 6.485 r_scangle_it 4.182 r_scbond_it 2.566 r_mcangle_it 1.698 r_angle_refined_deg 1.499 r_angle_other_deg 0.942 r_mcbond_it 0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.263 r_dihedral_angle_4_deg 17.488 r_dihedral_angle_3_deg 15.738 r_dihedral_angle_1_deg 6.485 r_scangle_it 4.182 r_scbond_it 2.566 r_mcangle_it 1.698 r_angle_refined_deg 1.499 r_angle_other_deg 0.942 r_mcbond_it 0.88 r_mcbond_other 0.196 r_chiral_restr 0.086 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.002 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 2371 Nucleic Acid Atoms Solvent Atoms 155 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing