9AXE

Cryo-EM reconstruction of a Staphylococcus aureus oleate hydratase (OhyA) assembly of dimers bound to a liposome

ELECTRON MICROSCOPY

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8UR3

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	15.643
r_lrange_other	15.643
r_dihedral_angle_6_deg	15.284
r_dihedral_angle_3_deg	13.184
r_scangle_it	8.065
r_scangle_other	8.065
r_mcangle_it	7.051
r_mcangle_other	7.051
r_dihedral_angle_1_deg	4.484
r_scbond_it	4.431
r_scbond_other	4.431
r_mcbond_it	4.102
r_mcbond_other	4.102
r_angle_refined_deg	1.073
r_dihedral_angle_2_deg	0.773
r_angle_other_deg	0.369
r_xyhbond_nbd_refined	0.221
r_symmetry_nbd_other	0.207
r_nbtor_refined	0.182
r_nbd_refined	0.176
r_symmetry_nbtor_other	0.076
r_symmetry_xyhbond_nbd_other	0.069
r_chiral_restr	0.048
r_bond_refined_d	0.004
r_gen_planes_refined	0.003
r_ncsr_local_group_4	0.003
r_ncsr_local_group_5	0.003
r_ncsr_local_group_6	0.003
r_ncsr_local_group_7	0.003
r_ncsr_local_group_8	0.003
r_ncsr_local_group_9	0.003
r_ncsr_local_group_16	0.003
r_ncsr_local_group_17	0.003
r_ncsr_local_group_18	0.003
r_ncsr_local_group_19	0.003
r_ncsr_local_group_20	0.003
r_ncsr_local_group_21	0.003
r_ncsr_local_group_30	0.003
r_ncsr_local_group_54	0.003
r_ncsr_local_group_55	0.003
r_ncsr_local_group_62	0.003
r_ncsr_local_group_63	0.003
r_ncsr_local_group_68	0.003
r_ncsr_local_group_69	0.003
r_ncsr_local_group_70	0.003
r_ncsr_local_group_73	0.003
r_ncsr_local_group_75	0.003
r_ncsr_local_group_76	0.003
r_ncsr_local_group_77	0.003
r_ncsr_local_group_79	0.003
r_ncsr_local_group_80	0.003
r_ncsr_local_group_81	0.003
r_ncsr_local_group_82	0.003
r_ncsr_local_group_84	0.003
r_ncsr_local_group_85	0.003
r_ncsr_local_group_2	0.002
r_ncsr_local_group_3	0.002
r_ncsr_local_group_10	0.002
r_ncsr_local_group_11	0.002
r_ncsr_local_group_14	0.002
r_ncsr_local_group_15	0.002
r_ncsr_local_group_22	0.002
r_ncsr_local_group_23	0.002
r_ncsr_local_group_26	0.002
r_ncsr_local_group_27	0.002
r_ncsr_local_group_28	0.002
r_ncsr_local_group_29	0.002
r_ncsr_local_group_31	0.002
r_ncsr_local_group_32	0.002
r_ncsr_local_group_33	0.002
r_ncsr_local_group_34	0.002
r_ncsr_local_group_35	0.002
r_ncsr_local_group_36	0.002
r_ncsr_local_group_37	0.002
r_ncsr_local_group_38	0.002
r_ncsr_local_group_39	0.002
r_ncsr_local_group_40	0.002
r_ncsr_local_group_41	0.002
r_ncsr_local_group_42	0.002
r_ncsr_local_group_43	0.002
r_ncsr_local_group_44	0.002
r_ncsr_local_group_45	0.002
r_ncsr_local_group_46	0.002
r_ncsr_local_group_47	0.002
r_ncsr_local_group_49	0.002
r_ncsr_local_group_51	0.002
r_ncsr_local_group_52	0.002
r_ncsr_local_group_53	0.002
r_ncsr_local_group_56	0.002
r_ncsr_local_group_58	0.002
r_ncsr_local_group_60	0.002
r_ncsr_local_group_61	0.002
r_ncsr_local_group_64	0.002
r_ncsr_local_group_66	0.002
r_ncsr_local_group_67	0.002
r_ncsr_local_group_71	0.002
r_ncsr_local_group_74	0.002
r_ncsr_local_group_78	0.002
r_ncsr_local_group_83	0.002
r_ncsr_local_group_86	0.002
r_ncsr_local_group_87	0.002
r_ncsr_local_group_88	0.002
r_ncsr_local_group_89	0.002
r_ncsr_local_group_90	0.002
r_gen_planes_other	0.001
r_ncsr_local_group_1	0.001
r_ncsr_local_group_12	0.001
r_ncsr_local_group_13	0.001
r_ncsr_local_group_24	0.001
r_ncsr_local_group_25	0.001
r_ncsr_local_group_48	0.001
r_ncsr_local_group_50	0.001
r_ncsr_local_group_57	0.001
r_ncsr_local_group_59	0.001
r_ncsr_local_group_65	0.001
r_ncsr_local_group_72	0.001
r_ncsr_local_group_91	0.001
r_bond_other_d

Sample
Assembly of dimers of OhyA bound to a liposome

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	87806
Reported Resolution (Å)	3.1
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1 (8UR3)
Refinement Space	REAL
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 BIOQUANTUM (6k x 4k)
Electron Dose (electrons/Å**2)	50

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TALOS ARCTICA
Minimum Defocus (nm)	500
Maximum Defocus (nm)	2500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS	2.7
Imaging Mode	BRIGHT FIELD
Specimen Holder Model	FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification	79000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	200
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC	4
MODEL FITTING	Coot
INITIAL EULER ASSIGNMENT	cryoSPARC	4
FINAL EULER ASSIGNMENT	cryoSPARC	4
CLASSIFICATION	cryoSPARC	4
RECONSTRUCTION	cryoSPARC	4
MODEL REFINEMENT	REFMAC

Image Processing
CTF Correction Type	CTF Correction Details	Number of Particles Selected	Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION