8QWC | pdb_00008qwc

Cryo-EM structure of Apo coproheme decarboxylase from Corynebacterium diphtheria.

ELECTRON MICROSCOPY

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6XUC

Refinement

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	18.338
r_lrange_other	18.335
r_dihedral_angle_6_deg	17.483
r_dihedral_angle_3_deg	16.811
r_scangle_it	13.924
r_scangle_other	13.923
r_mcangle_it	10.794
r_mcangle_other	10.794
r_scbond_it	9.283
r_scbond_other	9.282
r_mcbond_it	7.896
r_mcbond_other	7.887
r_dihedral_angle_2_deg	5.503
r_dihedral_angle_1_deg	4.8
r_angle_refined_deg	1.254
r_angle_other_deg	0.406
r_xyhbond_nbd_refined	0.228
r_symmetry_nbd_other	0.208
r_nbd_refined	0.196
r_nbtor_refined	0.194
r_symmetry_xyhbond_nbd_other	0.104
r_ncsr_local_group_1	0.096
r_ncsr_local_group_6	0.095
r_ncsr_local_group_4	0.093
r_ncsr_local_group_10	0.091
r_ncsr_local_group_2	0.089
r_ncsr_local_group_9	0.089
r_ncsr_local_group_5	0.087
r_ncsr_local_group_7	0.086
r_ncsr_local_group_3	0.083
r_symmetry_nbtor_other	0.08
r_ncsr_local_group_8	0.078
r_chiral_restr	0.058
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_gen_planes_other	0.001
r_bond_other_d

Sample
Structure of Apo coproheme decarboxylase from Corynebacterium diphtheria

Specimen Preparation
Sample Aggregation State	PARTICLE
Vitrification Instrument	FEI VITROBOT MARK IV
Cryogen Name	ETHANE
Sample Vitrification Details	Blotting time; 5.0-5.5 sec. Blotting force; 18 or 19.

3D Reconstruction
Reconstruction Method	SINGLE PARTICLE
Number of Particles	638556
Reported Resolution (Å)	2.27
Resolution Method	FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type	POINT
Point Symmetry	C5

Map-Model Fitting and Refinement
Id	1 (6XUC)
Refinement Space
Refinement Protocol	FLEXIBLE FIT
Refinement Target
Overall B Value
Fitting Procedure
Details

Data Acquisition
Detector Type	GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)	72

Imaging Experiment	1
Date of Experiment
Temperature (Kelvin)
Microscope Model	FEI TITAN KRIOS
Minimum Defocus (nm)	1000
Maximum Defocus (nm)	3000
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	105000
Calibrated Magnification
Source	FIELD EMISSION GUN
Acceleration Voltage (kV)	300
Imaging Details

EM Software
Task	Software Package	Version
PARTICLE SELECTION	cryoSPARC
IMAGE ACQUISITION	SerialEM
CTF CORRECTION	cryoSPARC
MODEL FITTING	MOLREP
CLASSIFICATION	cryoSPARC
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	REFMAC
MODEL REFINEMENT	PHENIX

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