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Crystal structure of the polyketide cyclase AknH with bound substrate and product analogue: implications for catalytic mechanism and product stereoselectivity.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F98 PDB entry 2F98
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 2.0M ammonium Chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.36 63.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 151.74 α = 90 b = 151.74 β = 90 c = 108.868 γ = 120
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 QUANTUM 4 2004-09-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.934 ESRF ID14-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 84.52 100 0.056 24.4 6.2 73655 73655 -3 25.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.95 98.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2F98 1.9 84.52 73655 69906 3713 99.96 0.18644 0.18536 0.20679 RANDOM 29.095
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] -0.73 -0.37 -0.73 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.791 r_dihedral_angle_4_deg 15.005 r_dihedral_angle_3_deg 14.888 r_dihedral_angle_1_deg 5.453 r_scangle_it 2.247 r_scbond_it 1.33 r_angle_refined_deg 1.19 r_mcangle_it 0.906 r_mcbond_it 0.552 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.791 r_dihedral_angle_4_deg 15.005 r_dihedral_angle_3_deg 14.888 r_dihedral_angle_1_deg 5.453 r_scangle_it 2.247 r_scbond_it 1.33 r_angle_refined_deg 1.19 r_mcangle_it 0.906 r_mcbond_it 0.552 r_nbtor_refined 0.306 r_nbd_refined 0.208 r_symmetry_vdw_refined 0.192 r_symmetry_hbond_refined 0.192 r_xyhbond_nbd_refined 0.152 r_chiral_restr 0.089 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4631 Nucleic Acid Atoms Solvent Atoms 459 Heterogen Atoms 175
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing