2024-03-13 REL RCSB RCSB RCSB 2018-07-31 2018-08-15 2018-08-15 2024-03-13 National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) R01AI136680-01 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM109524 United States National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) R01GM033050 United States Sub-2 Angstrom Ewald Curvature Corrected Single-Particle Cryo-EM Reconstruction of AAV-2 L336C Tan YZ Aiyer S AAV-2 L336C, Gene therapy, Ewald sphere curvature correction, Per particle CTF, VIRUS LIKE PARTICLE Tan YZ Aiyer S Mietzsch M Hull JA McKenna R Grieger J Samulski RJ Baker TS Agbandje-McKenna M Lyumkis D Sub-2 angstrom Ewald curvature corrected structure of an AAV2 capsid variant. Nat Commun UK 9 3628 3628 2018 30194371 doi:10.1038/s41467-018-06076-6 2041-1723 6e9d FULLOVERLAP Adeno-associated virus - 2 Adeno-associated virus - 2 0 1 Adeno-associated virus - 2 Homo sapiens 3.9 Icosahedral capsid 250.0 1 VIRUS-LIKE PARTICLE STRAIN false true Capsid protein VP1 Adeno-associated virus 2 Srivastava/1982 0.08202133599999999 60 Spodoptera frugiperda LEVO MAADGYLPDWLEDTLSEGIRQWWKLKPGPPPPKPAERHKDDSRGLVLPGYKYLGPFNGLDKGEPVNEADAAALEHDKAYD RQLDSGDNPYLKYNHADAEFQERLKEDTSFGGNLGRAVFQAKKRVLEPLGLVEEPVKTAPGKKRPVEHSPVEPDSSSGTG KAGQQPARKRLNFGQTGDADSVPDPQPLGQPPAAPSGLGTNTMATGSGAPMADNNEGADGVGNSSGNWHCDSTWMGDRVI TTSTRTWALPTYNNHLYKQISSQSGASNDNHYFGYSTPWGYFDFNRFHCHFSPRDWQRLINNNWGFRPKRLNFKLFNIQV KEVTQNDGTTTIANNCTSTVQVFTDSEYQLPYVLGSAHQGCLPPFPADVFMVPQYGYLTLNNGSQAVGRSSFYCLEYFPS QMLRTGNNFTFSYTFEDVPFHSSYAHSQSLDRLMNPLIDQYLYYLSRTNTPSGTTTQSRLQFSQAGASDIRDQSRNWLPG PCYRQQRVSKTSADNNNSEYSWTGATKYHLNGRDSLVNPGPAMASHKDDEEKFFPQSGVLIFGKQGSEKTNVDIEKVMIT DEEEIRTTNPVATEQYGSVSTNLQRGNRQAATADVNTQGVLPGMVWQDRDVYLQGPIWAKIPHTDGHFHPSPLMGGFGLK HPPPQILIKNTPVPANPSTTFSAAKFASFITQYSTGQVSVEIEWELQKENSKRWNPEIQYTSNYNKSVNVDFTVDTNGVY SEPRPIGTRYLTRNL P03135 water 1.8015e-05 11820 HOH singleParticle particle 1.7 7.4 150.0 NaCl sodium chloride 2.0 MgCl2 magnesium chloride 50.0 C8H18N2O4S HEPES Quantifoil, UltrAuFoil, R1.2/1.3 GOLD 300 HOLEY PLASMA CLEANING OTHER ETHANE 80 277 HOMEMADE PLUNGER
Double blotting was used to increase particle concentration. Sample was added to a plasma-cleaned (Gatan Solarus) grid and blotted away using Whatman grade 4 filter paper after 20 second wait time..
FEI TITAN KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 70.0 2.7 0.6 2.0 37000.0 FEI TITAN KRIOS AUTOGRID HOLDER NITROGEN
Beam tilt in 8 directions +/- 5 mrad
GATAN K2 SUMMIT (4k x 4k) SUPER-RESOLUTION 3838 3710 5-19 1 1317 3.5 22.5
Stage shift mode for data collection
 1
super-resolution mode
78194
Template-based picking by generating template from a 2-D classification of an initial subset of data.
 Ab initio model generated using CryoSPARC. I FOURIER SPACE 1.86 FSC 0.143 CUT-OFF FREALIGN 9.11
Frequency limited refinement
30515 PROJECTION MATCHING cryoSPARC 0.65 PROJECTION MATCHING FREALIGN 9.11 emd_9012.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 720 720 720 0 0 0 720 720 720 283.68 283.68 283.68 90.0 90.0 90.0 X Y Z -0.22251815 0.41616842 0.0019748327 0.02993493 0.394 0.394 0.394 0.06 AUTHOR Final map reconstructed with a box of 800, clipped to 360, and then resampled to 720 pixels 1LP3 PDB experimental model RIGID BODY FIT Correlation coefficient, EM ringer score REAL 61.899999999999999 emd_9012_additional_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 359 359 359 0 0 0 359 359 359 282.892 282.892 282.892 90.0 90.0 90.0 X Y Z 0.0 1.0000001 0.22148526 0.3675184 0.788 0.788 0.788 AUTHOR Raw 3D FSC volume generated from the half maps emd_9012_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 283.68 283.68 283.68 90.0 90.0 90.0 X Y Z -0.013495815 0.042843092 0.000017371556 0.0043832446 0.788 0.788 0.788 AUTHOR First half map reconstructed with a box of 800, clipped to 360 pixels emd_9012_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 360 360 360 0 0 0 360 360 360 283.68 283.68 283.68 90.0 90.0 90.0 X Y Z -0.012406162 0.042423658 0.000019641555 0.004384281 0.788 0.788 0.788 AUTHOR Second half map reconstructed with a box of 800, clipped to 360 pixels