9H99 | pdb_00009h99

Native structure of the full-length pesticidal protein Cry1Ca18 at pH7, from crystals formed in vivo

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	4W8J	Cry1Ac

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	IN CELL	9	298	Naturally grown

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.69

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.16	α = 90
b = 88.16	β = 90
c = 266.43	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	298	PIXEL	AGIPD		2023-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	FREE ELECTRON LASER	EUROPEAN XFEL BEAMLINE SPB/SFX	1.33	European XFEL	SPB/SFX

Serial Crystallography

Sample delivery method
Diffraction ID	Description	Sample Delivery Method
1		injection

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.8	36.19	100	0.9965445	13.75	207.97		98288

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.82	100		0.79	2.77

Refinement

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 (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	1.8	36.19	93379	4841	99.98	0.18353	0.18157	0.1894	0.22169	0.2286	RANDOM	18.835

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]
-0.56			-0.56		1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.574
r_dihedral_angle_1_deg	6.863
r_dihedral_angle_2_deg	6.482
r_long_range_B_refined	4.853
r_long_range_B_other	4.807
r_angle_refined_deg	1.743
r_scangle_other	1.351
r_scbond_it	0.824
r_scbond_other	0.822
r_mcangle_it	0.807
r_mcangle_other	0.807
r_angle_other_deg	0.613
r_mcbond_it	0.458
r_mcbond_other	0.458
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_dihedral_angle_4_deg
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	8493
Nucleic Acid Atoms
Solvent Atoms	809
Heterogen Atoms	2

Software

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