MD trajectory. The coordinates of the OGT–UDP–peptide complex (PDB 3PE4) were optimized in the Protein Preparation Wizard (Schrodinger 2009) where hydrogens were added; water molecules, UDP and peptide were stripped; and the structure was minimized using the OPLS2001 forcefield. The 1-μm simulation used the CHARM27 forcefield46, and the simple point charge model for water47. The CHARM27 forcefield was applied to the system using the VIPARR utility. The default Desmond relaxation was performed before simulation, and molecular dynamics were run at constant temperature (300 K) and pressure (1 bar). The simulation was performed by using the program Desmond, version 2.2.9.1.030 compiled by SBGrid on an optimized 64-node Linux-based InfiniBand cluster and took 75 days to complete. Molecular dynamics trajectories were processed and animated with VMD48.
Data DOI: 10.15785/SBGRID/190 | PDB ID 3PE4: RCSB PDBe | Publication DOI: 10.1038/nature09638 | Published: 3 Nov 2015
Sliz Laboratory, Harvard Medical School
Native dataset.
Data DOI: 10.15785/SBGRID/189 | PDB ID 4ZXS: RCSB PDBe | Publication DOI: 10.15252/embj.201592359 | Published: 30 Oct 2015
Heldwein Laboratory, Tufts University School of Medicine
Soluble portion of pseudorabies virus nuclear egress complex.
Data DOI: 10.15785/SBGRID/188 | PDB ID 4Z3U: RCSB PDBe | Publication DOI: 10.15252/embj.201592359 | Published: 30 Oct 2015
Heldwein Laboratory, Tufts University School of Medicine
mSlice Conditions: Waveform type : Linear X Galvo Offset, Interval (um), # of Pixels for Excitation (0) : 0 0.1 51 Z Galvo Offset, Interval (um), # of Pixels for Excitation (0) : -0.599257 0 251 Z PZT Offset, Interval (um), # of Pixels for Excitation (0) : 26 0 251 S PZT Offset, Interval (um), # of Pixels for Excitation (0) : 50 0.398406 251 # of stacks (0) : 200 Excitation Filter, Laser, Power (%), Exp(ms) (0) : N/A 488 20 40 Cycle lasers : per Z Z motion : Sample piezo
Data DOI: 10.15785/SBGRID/187 | Published: 16 Oct 2015
Kirchhausen Laboratory, Children's Hospital Boston
Bovine catalase microcrystals solved by MicroED
Data DOI: 10.15785/SBGRID/186 | PDB ID 3J7B: RCSB PDBe | Publication DOI: 10.7554/eLife.01345 | Published: 13 Oct 2015
Gonen Laboratory, University of California, Los Angeles
Native dataset
Data DOI: 10.15785/SBGRID/184 | Publication DOI: 10.1021/jm501120z | Published: 23 Oct 2015
Blacklow Laboratory, Harvard Medical School
SeMet data, collected on two separate spots on a single crystal
Data DOI: 10.15785/SBGRID/182 | PDB ID 4FHM: RCSB PDBe | Publication DOI: 10.1073/pnas.1205151109 | Published: 6 Oct 2015
Schwartz Laboratory, Massachusetts Institute of Technology
native data, collected on four spots on the same crystal
Data DOI: 10.15785/SBGRID/181 | PDB ID 4FHM: RCSB PDBe | Publication DOI: 10.1073/pnas.1205151109 | Published: 6 Oct 2015
Schwartz Laboratory, Massachusetts Institute of Technology
Ta6Br12 derivative data
Data DOI: 10.15785/SBGRID/180 | PDB ID 4FHN: RCSB PDBe | Publication DOI: 10.1073/pnas.1205151109 | Published: 6 Oct 2015
Schwartz Laboratory, Massachusetts Institute of Technology
native data, collected in two separate spots
Data DOI: 10.15785/SBGRID/179 | PDB ID 4FHN: RCSB PDBe | Publication DOI: 10.1073/pnas.1205151109 | Published: 6 Oct 2015
Schwartz Laboratory, Massachusetts Institute of Technology
native data
Data DOI: 10.15785/SBGRID/178 | PDB ID 4FCC: RCSB PDBe | Publication DOI: 10.1073/pnas.1205151109 | Published: 6 Oct 2015
Schwartz Laboratory, Massachusetts Institute of Technology
immature NTD domain (one extra residue at the N-terminus, before the mature Pro) / SAD dataset (quick iodide soak) collected at Cu Ka wavelength
Data DOI: 10.15785/SBGRID/177 | PDB ID 4PH3: RCSB PDBe | Publication DOI: 10.1126/science.aaa5182 | Published: 6 Oct 2015
Buschiazzo Laboratory, Institut Pasteur de Montevideo
SeMet dataset, all proteins derivatized
Data DOI: 10.15785/SBGRID/176 | Publication DOI: 10.1038/nsmb.2998 | Published: 25 Sep 2015
Schwartz Laboratory, Massachusetts Institute of Technology
SeMet dataset, Nup85 derivatized only
Data DOI: 10.15785/SBGRID/175 | PDB ID 4YCZ: RCSB PDBe | Publication DOI: 10.1038/nsmb.2998 | Published: 25 Sep 2015
Schwartz Laboratory, Massachusetts Institute of Technology
Native dataset
Data DOI: 10.15785/SBGRID/174 | PDB ID 4ZI8: RCSB PDBe | Publication DOI: 10.1016/j.str.2015.09.005 | Published: 27 Oct 2015
Gaudet Laboratory, Harvard University
Native dataset
Data DOI: 10.15785/SBGRID/173 | PDB ID 4ZI9: RCSB PDBe | Publication DOI: 10.1016/j.str.2015.09.005 | Published: 27 Oct 2015
Gaudet Laboratory, Harvard University
native data set
Data DOI: 10.15785/SBGRID/172 | PDB ID 4PH1: RCSB PDBe | Publication DOI: 10.1126/science.aaa5182 | Published: 8 Sep 2015
Buschiazzo Laboratory, Institut Pasteur de Montevideo
mature NTD domain / native data
Data DOI: 10.15785/SBGRID/171 | PDB ID 4PH2: RCSB PDBe | Publication DOI: 10.1126/science.aaa5182 | Published: 8 Sep 2015
Buschiazzo Laboratory, Institut Pasteur de Montevideo
native (non-engineered) construct of full-length capsid
Data DOI: 10.15785/SBGRID/169 | PDB ID 4PH0: RCSB PDBe | Publication DOI: 10.1126/science.aaa5182 | Published: 8 Sep 2015
Buschiazzo Laboratory, Institut Pasteur de Montevideo
