Parallel Fine Sampling to Solve Large or Difficult Structures Manually exploring large parameter space to find right combination of parameters is time-

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Parallel Fine Sampling to Solve Large or Difficult Structures Manually exploring large parameter space to find right combination of parameters is time- consuming and frustrating. It often results in giving up on an otherwise solvable structure. Parallel exploration of parameter space is an effective approach to solve challenging structures efficiently and reliably –Systematically explore parameter space –Speed up with parallel execution on PC cluster xxx

Structures Solved by Fine Grid Search TargetMol/ASUSites/MolSitesSpace Group Resolution MB3864A4624P PE000293D6954H32.15 PD06751F61484P TB1547G81296P PC06751C620120P FJ5490C12672P12.00 FH7599A* C22.00 *work in progress

PD06751F 454aa/15 Met, 1.9Å P , hexamer in asu Space group choices narrowed down by systematic absence 1080 SHELXD jobs (200 trials each), parameters explored: –E value cutoff ( /0.1) –Number of sites (40-120/10) –Resolution cutoff ( /0.1) 3.5 hrs to finish all 1080 jobs on SDC cluster (220 CPUs) Of 1080 jobs, 39% find correct heavy atom solutions First correct solution within minutes, 84/84 sites found

PE00293D 285aa/11 Met, H3, 2.15Å, hexamer/asu, 2 wavelength MAD, PDB id: 2p SHELXD jobs (200 trials each), parameters explored: –E value cutoff ( /0.1) –Number of sites (20-90/10) –Resolution cutoff ( /0.1) 1 hrs to finish all 760 jobs on SDC cluster (220 CPUs) Solutions are rare, only 12 jobs (out of 760 jobs, 1.5%) find correct heavy atom solutions, 53/54 sites found

TB1547G 409aa (13 Met)/monomer, P , 2 tetramers per asu Initially labeled as something else (TB5131A, 179aa/2 Met) Treated as an unknown target POINTLESS and XPREP to narrow down space group choices, XPREP to generate FA values SHELXD Grid search: –Sites in step of 10 –Resolution cutoff in step of 0.1 –E value cutoff from in step of parallel SHELXD jobs, each SHELXD job attempts 200 trials The job order is randomized to uniformly sample the search space initially Solutions appeared usually appears in minutes, so jobs can be terminated early if necessary Each SHELXD job needs ~1hrs, ~2 hrs for all jobs to finish on SDC cluster (220 CPUs) Interpretation of density map gave correct identification of the target

FH7599A: MR+MAD Estimated monomers per asu, Heavy atom sites No highly homologous (>20% seq id) MR models FFAS or PSI-BLAST identified a remote sequence homolog TM0064 (14% seq id) TM0064 trimer poly-alanine is used as MR model, use of the trimer as MR template significantly improved signal to noise in MR procedure Density modification is critical for improving MR phases Improved DM phases + MAD data to locate ~200 heavy atom sites and MAD phasing rmsd 2.42 Å for 82% C  FH7599A vs TM0064