8Q6I | pdb_00008q6i

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	8QRE	stripped of solvent and ligand molecules, used one copy of the holotoxin (1 A subunit, 5 B subunits) as the search model

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293.15	Crystallization mix: 20% PEG6000 0.2 M lithium chloride 0.1 M Tris pH 8.0 Protein storage buffer: 0.05 M Tris/HCl pH 7.5 0.2 M NaCl

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.35

Symmetry
Space Group	P 1 21 1

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 9M		2022-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID30B	0.87313	ESRF	ID30B

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.6	48.84	96.71	0.085	0.092	0.034	0.999	10.8	7.1		95507			29.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.66	92.1		2.808	3.022	1.108	0.436	0.7	7.4

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.603	48.84	94960	4607	96.709	0.187	0.185	0.1942	0.2215	0.2297	28.494

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.734		-0.793	2.226		-0.874

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.691
r_dihedral_angle_3_deg	12.53
r_dihedral_angle_1_deg	7.248
r_lrange_it	5.87
r_lrange_other	5.87
r_scangle_it	4.399
r_scangle_other	4.399
r_mcangle_other	3.513
r_mcangle_it	3.507
r_scbond_it	2.943

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.691
r_dihedral_angle_3_deg	12.53
r_dihedral_angle_1_deg	7.248
r_lrange_it	5.87
r_lrange_other	5.87
r_scangle_it	4.399
r_scangle_other	4.399
r_mcangle_other	3.513
r_mcangle_it	3.507
r_scbond_it	2.943
r_scbond_other	2.942
r_dihedral_angle_2_deg	2.811
r_mcbond_it	2.471
r_mcbond_other	2.462
r_angle_refined_deg	1.487
r_angle_other_deg	0.524
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.214
r_symmetry_nbd_other	0.193
r_nbd_other	0.18
r_nbtor_refined	0.175
r_symmetry_nbd_refined	0.134
r_ncsr_local_group_4	0.095
r_ncsr_local_group_1	0.094
r_ncsr_local_group_3	0.089
r_metal_ion_refined	0.087
r_ncsr_local_group_2	0.087
r_symmetry_xyhbond_nbd_refined	0.085
r_chiral_restr	0.078
r_symmetry_nbtor_other	0.078
r_ncsr_local_group_8	0.074
r_symmetry_xyhbond_nbd_other	0.073
r_ncsr_local_group_10	0.07
r_ncsr_local_group_9	0.067
r_ncsr_local_group_5	0.066
r_ncsr_local_group_6	0.061
r_ncsr_local_group_7	0.055
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5885
Nucleic Acid Atoms
Solvent Atoms	408
Heterogen Atoms	82

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