9G7M | pdb_00009g7m

Crystal structure of Collimonas fungivorans PE-like toxin, Cfx

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1IKQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	294.15	0.2 M Magnesium chloride hexahydrate 0.1 M BIS-Tris pH 5.5, 25 % w/v PEG 3350 (condition H11 of the JCSG-plus Screen, Molecular Dimensions)

Crystal Properties
Matthews coefficient	Solvent content
4.31	71.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 141.797	α = 90
b = 141.797	β = 90
c = 202.661	γ = 120

Symmetry
Space Group	P 62 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	100	PIXEL	DECTRIS EIGER2 XE 16M		2021-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

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	2.8	70.9	100	0.493	0.5	0.109	0.998	7.6	39.6		30359

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	2.8	2.95	100		5.74	5.87	1.257	0.439	0.9	41.2

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.8	70.9	30302	1483	99.951	0.23	0.2291	0.2304	0.2531	0.2547	83.992

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]
0.519	0.259		0.519		-1.683

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.252
r_dihedral_angle_6_deg	12.881
r_lrange_it	7.936
r_lrange_other	7.936
r_dihedral_angle_1_deg	6.638
r_mcangle_it	4.999
r_mcangle_other	4.999
r_dihedral_angle_2_deg	4.685
r_scangle_it	4.609
r_scangle_other	4.608
r_mcbond_it	2.89
r_mcbond_other	2.887
r_scbond_it	2.591
r_scbond_other	2.591
r_angle_refined_deg	0.898
r_symmetry_nbd_refined	0.437
r_angle_other_deg	0.302
r_nbd_refined	0.21
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.174
r_nbd_other	0.153
r_xyhbond_nbd_refined	0.129
r_symmetry_nbtor_other	0.076
r_chiral_restr	0.041
r_bond_refined_d	0.003
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4699
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms	1

Software

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