5L1D | pdb_00005l1d

Structure of rabbit RyR2 in complex with FKBP12.6 in a closed state (conformation C1)


ELECTRON MICROSCOPY

Refinement

RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.548
r_long_range_B_refined26.965
r_long_range_B_other26.965
r_dihedral_angle_3_deg16.038
r_dihedral_angle_4_deg11.316
r_mcangle_it11.282
r_mcangle_other11.282
r_scangle_other6.885
r_dihedral_angle_1_deg6.52
r_mcbond_it6.408
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.548
r_long_range_B_refined26.965
r_long_range_B_other26.965
r_dihedral_angle_3_deg16.038
r_dihedral_angle_4_deg11.316
r_mcangle_it11.282
r_mcangle_other11.282
r_scangle_other6.885
r_dihedral_angle_1_deg6.52
r_mcbond_it6.408
r_mcbond_other6.408
r_scbond_it3.294
r_scbond_other3.294
r_angle_refined_deg1.281
r_angle_other_deg1.044
r_chiral_restr0.065
r_bond_refined_d0.016
r_gen_planes_refined0.004
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
Ryanodine Receptor - FKBP12.6
Specimen Preparation
Sample Aggregation StatePARTICLE
Vitrification InstrumentFEI VITROBOT MARK IV
Cryogen NameETHANE
Sample Vitrification DetailsBlot for 2 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
3D Reconstruction
Reconstruction MethodSINGLE PARTICLE
Number of Particles13158
Reported Resolution (Å)11
Resolution MethodFSC 0.5 CUT-OFF
Other DetailsFREALIGN half maps were used to calculate FSC.
Refinement Type
Symmetry TypePOINT
Point SymmetryC4
Map-Model Fitting and Refinement
Id1
Refinement SpaceRECIPROCAL
Refinement ProtocolRIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector TypeFEI FALCON II (4k x 4k)
Electron Dose (electrons/Å**2)20
Imaging Experiment1
Date of Experiment
Temperature (Kelvin)
Microscope ModelFEI TITAN KRIOS
Minimum Defocus (nm)2000
Maximum Defocus (nm)6000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS2.7
Imaging ModeBRIGHT FIELD
Specimen Holder ModelFEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification59000
Calibrated Magnification62000
SourceFIELD EMISSION GUN
Acceleration Voltage (kV)300
Imaging Details
EM Software
TaskSoftware PackageVersion
PARTICLE SELECTIONRELION1.3
IMAGE ACQUISITIONEPU
CTF CORRECTIONCTFFIND3.5
CTF CORRECTIONFREALIGN9.11
MODEL FITTINGSitus2.8
MODEL FITTINGUCSF Chimera1.11
MODEL REFINEMENTREFMAC5.8
INITIAL EULER ASSIGNMENTFREALIGN9.11
FINAL EULER ASSIGNMENTFREALIGN9.11
RECONSTRUCTIONFREALIGN9.11
Image Processing
CTF Correction TypeCTF Correction DetailsNumber of Particles SelectedParticle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION13600Used Relion 1.3 to auto-pick the particles. Inspected each micrograph for false positives.