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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 1SJW PDB entry 1SJW
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 3.4 63.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.271 α = 90 b = 152.271 β = 90 c = 109.43 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 MAR CCD 165 mm 2003-12-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-3 0.931 ESRF ID14-3
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 56.48 100 55241 55241 -3
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 2.1 2.2 100
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1SJW 2.1 56.48 55241 52433 2804 100 0.19469 0.19342 0.21838 0.1968 RANDOM 29.42
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] -0.82 -0.41 -0.82 1.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.637 r_scangle_it 2.451 r_scbond_it 1.517 r_angle_refined_deg 1.17 r_mcangle_it 1.03 r_mcbond_it 0.55 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.144
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 5.637 r_scangle_it 2.451 r_scbond_it 1.517 r_angle_refined_deg 1.17 r_mcangle_it 1.03 r_mcbond_it 0.55 r_symmetry_hbond_refined 0.223 r_nbd_refined 0.204 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.085 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4631 Nucleic Acid Atoms Solvent Atoms 245 Heterogen Atoms 132
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing