7KZ7 | pdb_00007kz7

Crystals Structure of the Mutated Protease Domain of Botulinum Neurotoxin X (X4130B1).

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6F47

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	277	Protein: 10mg/ml, 20 mM Tris, pH 7.5, 200 mM NaCl; Screen: 0.1 M Bis-Tris, pH 6.5, 20% PEG 5000; Cryo: 10% glycerol, 0.1 M Bis-Tris, pH 6.5, 20% PEG 5000.

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.935	α = 90
b = 86.775	β = 90
c = 93.557	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD	Be	2020-02-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	1.8	30	100	0.061	0.061	0.066	0.024	31	7.2		46066		-3	25.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.83	100		0.779	0.779	0.841	0.314	0.856	2.6	7.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	6F47	1.8	29.97	43595	2356	99.97	0.1525	0.1507	0.16	0.1846	0.19	RANDOM	28.768

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]
2.97			-1.71		-1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.166
r_dihedral_angle_4_deg	11.004
r_dihedral_angle_3_deg	9.112
r_dihedral_angle_1_deg	3.826
r_angle_refined_deg	1.353
r_angle_other_deg	0.356
r_chiral_restr	0.065
r_gen_planes_refined	0.054
r_gen_planes_other	0.048
r_bond_refined_d	0.006

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.166
r_dihedral_angle_4_deg	11.004
r_dihedral_angle_3_deg	9.112
r_dihedral_angle_1_deg	3.826
r_angle_refined_deg	1.353
r_angle_other_deg	0.356
r_chiral_restr	0.065
r_gen_planes_refined	0.054
r_gen_planes_other	0.048
r_bond_refined_d	0.006
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3399
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	41

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.