Item 1: October 2005 Publications by Members:

1:  Tang C, Iwahara J, Clore GM.
 Accurate Determination of Leucine and Valine Side-chain Conformations using U-[(15)N/(13)C/(2)H]/[(1)H-(methine/methyl)-Leu/Val] Isotope Labeling, NOE Pattern Recognition, and Methine Cgamma Hgamma/Cbeta-Hbeta Residual Dipolar Couplings: Application to the 34-kDa Enzyme IIA(Chitobiose).
J Biomol NMR. 2005 Oct;33(2):105-21. PMID: 16258829

2:  Gan J, Tropea JE, Austin BP, Court DL, Waugh DS, Ji X.
 Intermediate states of ribonuclease III in complex with double-stranded RNA.
Structure (Camb). 2005 Oct;13(10):1435-42. PMID: 16216575

3:  Lee JY, Chang J, Joseph N, Ghirlando R, Rao DN, Yang W.
 MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage.
Mol Cell. 2005 Oct 7;20(1):155-66. PMID: 16209953

4:  Ronning DR, Guynet C, Ton-Hoang B, Perez ZN, Ghirlando R, Chandler M, Dyda F.
 Active site sharing and subterminal hairpin recognition in a new class of DNA transposases.
Mol Cell. 2005 Oct 7;20(1):143-54. PMID: 16209952

5:  Phan J, Austin BP, Waugh DS.
 Crystal structure of the Yersinia type III secretion protein YscE.
Protein Sci. 2005 Oct;14(10):2759-63. PMID: 16195558

6:  Zhou T, Hamer DH, Hendrickson WA, Sattentau QJ, Kwong PD.
 Interfacial metal and antibody recognition.
PNAS USA. 2005 Oct 11;102(41):14575-80. PMID: 16195378

7:  Phan J, Shi ZD, Burke TR Jr, Waugh DS.
 Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain.
J Mol Biol. 2005 Oct 14;353(1):104-15. PMID: 16165154

8:  Ramasamy V, Ramakrishnan B, Boeggeman E, Ratner DM, Seeberger PH, Qasba PK.
 Oligosaccharide preferences of beta1,4-galactosyltransferase-I: crystal
structures of Met340His mutant of human beta1,4-galactosyltransferase-I with a pentasaccharide and trisaccharides of the N-glycan moiety.
J Mol Biol. 2005 Oct 14;353(1):53-67. PMID: 16157350

9:  Bradley CM, Ronning DR, Ghirlando R, Craigie R, Dyda F.
 Structural basis for DNA bridging by barrier-to-autointegration factor.
Nat Struct Mol Biol. 2005 Oct;12(10):935-6. PMID: 16155580

10:  Dauter Z.
 Efficient use of synchrotron radiation for macromolecular diffraction data
collection.
Prog Biophys Mol Biol. 2005 Oct;89(2):153-72. Review. PMID: 15910916

11:  Hall TM.
 Structure and function of argonaute proteins.
Structure (Camb). 2005 Oct;13(10):1403-8. PMID: 16216572

Item 2: Tips and Tricks

This section is always open for contributions. Click for Introduction and tips and tricks in Crystallization, Derivatization, Diffraction, Symmetry, Structure Solution, Structure Refinement, and Structure Analysis.

Recommended Review: "Post-crystallization treatments for improving diffraction quality of protein crystals" by Begona Hera and Jennifer L. Martin

Item 3: Topic Discussion

PHASER: MR with Maximum Likelihood

Xinhua Ji (NCI): All Data and Small Search Models

My group has solved about 10 structures using PHASER. Our limited experience suggests the use of all data and small search models. At higher resolution, the solution is more likely unique. Small models are often solid and likely more accurate. Below is a script for the first, and often successful, MR attempt with PHASER, where protein-1 contains a single domain while protein-2 contains two different domains.

phaser << eof > auto.log           # PHASER v1.3

TITLe  your-project automatic

MODE MR_AUTO

HKLIn your-data.mtz

LABIn F=FP SIGF=SIGFP

ENSEmble model-1  PDBfile model-1.pdb  IDENtity 95

ENSEmble model-2a PDBfile model-2a.pdb IDENtity 90

ENSEmble model-2b PDBfile model-2b.pdb IDENtity 90

COMPosition PROTein MW 32000 NUM 1 # protein-1

COMPosition PROTein MW 66000 NUM 1 # protein-2

SEARch ENSEmble model-1  NUM 1

SEARch ENSEmble model-2a NUM 1

SEARch ENSEmble model-2b NUM 1

ROOT auto

eof

Multiple search models (as shown below) help, especially when the search model is not that solid, as indicated by high B factors (of each model), high RMS values (between the models), and low sequence identity (to the unknown).

ENSEmble model-2b PDBfile model-2b1.pdb IDENtity 90 &

                  PDBfile model-2b2.pdb IDENtity 90 &

                  PDBfile model-2b3.pdb IDENtity 90

Click for previous discussions on: PHASER, HKL2000, Parallel Protein Expression, Structural Genomics, NCS, Missing Atoms, Trends in Crystallography, and Absorption Correction.

Item 4: Lectures

Dr. Zbigniew Dauter's Lectures at the NIH (03/29-31)