1 Molecular Replacement crystal homologous model Rotation Function crystal and Patterson map model and Patterson map2 Rotation Function – Multiply Patterson Maps 0° rotation 45° rotation 90° rotation Translation Function Evaluate (with Rcrys) Rotated Model at Each Position in Cell High Rcrys High Rcrys Low Rcrys3 Assessing MIR/MAD maps 1. The map should have interpretable features, e.g. helices and sheets. 2. Phasing statistics should have more signal than noise: |FH| > lack of closure error, xαp FOM > 0.5 3. Correct hand is evident. E = [Σh |FH| / xαp] / N Assessing Molecular Replacement maps The map should have interpretable features for atoms not included in the original model, e.g. omitted side chains or bound ligands4 Phase Improvement Macromolecular crystallography relies on known chemistry for success Examples: • Symmetry averaging • Solvent flattening • Model restraints • Known sequence Solvent Flattening / Symmetry Averaging • Find molecular boundaries • Set solvent to zero • Restrict large peaks • Average around non-crystallographic symmetry • Back Fourier Transform5 Improved Map Model Building 1. Using a program such as Coot, trace the chain and build the model, using the known sequence 2. If the map is excellent, use an automatic model building program such as ARP/wARP 3. Use the model to improve the
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