4ZKT | pdb_00004zkt

Crystal structure of the progenitor M complex of Clostridium botulinum type E neurotoxin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FFZ	3FFZ, 3V0A
experimental model	PDB	3V0A	3FFZ, 3V0A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	294	5.0ul sample was equilibrated against 600ul of 6 - 8% PEG 4000 and 0.1M sodium acetate of pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.77	67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 192.601	α = 90
b = 192.601	β = 90
c = 286.538	γ = 120

Symmetry
Space Group	P 31

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	ADSC QUANTUM 315		2013-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	3	50	69.8	2.3	4.5		165586			110.6

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	3FFZ, 3V0A	3.05	49.3	133607	1334	59.72	0.24415	0.24338	0.25	0.32083	0.31	RANDOM	134.999

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]
1.03	1.03		1.03		-3.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.42
r_long_range_B_refined	30.731
r_long_range_B_other	30.731
r_scangle_other	21.831
r_mcangle_it	19.914
r_mcangle_other	19.914
r_dihedral_angle_3_deg	18.734
r_dihedral_angle_4_deg	17.001
r_scbond_it	12.958
r_scbond_other	12.957
r_mcbond_it	12.49
r_mcbond_other	12.488
r_dihedral_angle_1_deg	7.841
r_angle_refined_deg	1.438
r_angle_other_deg	0.94
r_chiral_restr	0.073
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.004
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

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	56949
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	3

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing