6T14 | pdb_00006t14

Native structure of mosquitocidal Cyt1A protoxin obtained by Serial Femtosecond Crystallography on in vivo grown crystals at pH 7

X-RAY DIFFRACTION

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Serial Crystallography (SX)

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RON

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL		300	In cell crystallization by recombinant expression in a Bacillus thuringiensis serovar israelensis strain devoid of its pBt plasmid.

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.781	α = 90
b = 64.781	β = 90
c = 164.482	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	300	PIXEL	CS-PAD CXI-2		2018-11-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	SLAC LCLS BEAMLINE CXI	1.28	SLAC LCLS	CXI

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Measurement
Diffraction ID	Pulse Duration	Pulse Repetition Rate	Focal Spot Size	Pulse Energy	Photons Per Pulse
1	40 (fs)	120	1.7	undefined (KeV)

Data Reduction
Diffraction ID	Frames Indexed	Crystal Hits	Frames Indexed	Latices Merged
1	8462		8462

Injection
Diffraction ID	Description	Flow Rate	Injector Diameter	Injection Power	Injector Nozzle	Filter Size	Carrier Solvent
1	MESH	undefined (µl/min)	undefined (µm)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	R Split (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	1.86	50	98.7	0.995	0.125	18.6	107.8		17966

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.86	1.89	100		0.078	0.877	1.6	17.96

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3ron	1.86	26.549	16944	845	94.254	0.22	0.2179	0.22	0.2559	0.26	29.343

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]
-0.014	-0.007		-0.014		0.047

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.228
r_dihedral_angle_3_deg	14.581
r_dihedral_angle_1_deg	6.252
r_lrange_it	5.08
r_dihedral_angle_4_deg	5.074
r_lrange_other	4.259
r_scangle_it	1.709
r_scangle_other	1.709
r_mcangle_it	1.616
r_mcangle_other	1.616
r_angle_other_deg	1.404
r_scbond_it	1.04
r_scbond_other	1.039
r_mcbond_it	0.945
r_mcbond_other	0.944
r_angle_refined_deg	0.884
r_symmetry_nbd_other	0.22
r_nbd_refined	0.199
r_nbd_other	0.186
r_nbtor_refined	0.167
r_xyhbond_nbd_refined	0.157
r_symmetry_nbd_refined	0.137
r_symmetry_xyhbond_nbd_refined	0.118
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.071
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_gen_planes_other	0.003
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1882
Nucleic Acid Atoms
Solvent Atoms	245
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
DIALS	data scaling
PHASER	phasing