9UEJ | pdb_00009uej

Cryo-EM structure of L-lysine 6-dehydrogenase

ELECTRON MICROSCOPY

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Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.061
r_long_range_B_refined	24.611
r_long_range_B_other	24.61
r_dihedral_angle_4_deg	20.639
r_scangle_other	19.232
r_dihedral_angle_3_deg	13.697
r_scbond_it	11.111
r_scbond_other	11.11
r_mcangle_other	10.183
r_mcangle_it	10.18
r_mcbond_it	6.116
r_mcbond_other	6.109
r_dihedral_angle_1_deg	4.356
r_angle_other_deg	1.488
r_angle_refined_deg	1.221
r_chiral_restr	0.065
r_bond_other_d	0.033
r_bond_refined_d	0.01
r_gen_planes_refined	0.009
r_gen_planes_other	0.008
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
L-lysine 6-dehydrogenase

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument
Cryogen Name	ETHANE
Sample Vitrification Details

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	761921
Reported Resolution (Å)	2.94
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT

Map-Model Fitting and Refinement
Id	1
Refinement Space
Refinement Protocol
Refinement Target
Overall B Value
Fitting Procedure
Details

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

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	JEOL CRYO ARM 300
Minimum Defocus (nm)	800
Maximum Defocus (nm)	1500
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
Imaging Mode	BRIGHT FIELD
Specimen Holder Model
Nominal Magnification
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	RELION	4.0.1
MODEL REFINEMENT	REFMAC	5.8.0267
RECONSTRUCTION	RELION	4.0.1

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