8CJH | pdb_00008cjh

Architecture of a PKS-NRPS hybrid megaenzyme involved in the biosynthesis of the genotoxin colibactin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	0.1 M MES pH 6.5, 19 % PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 187.643	α = 90
b = 233.374	β = 90
c = 256.598	γ = 90

Symmetry
Space Group	C 2 2 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	PIXEL	DECTRIS PILATUS3 2M		2021-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.9655	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.98	49.395	93.6	0.138	0.996	9.5	2		114296

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.98	3.088			1.05	0.522	1.6

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	2.982	49.395	78289	1940	68.481	0.218	0.2171	0.22	0.2384	0.24	95.226

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			0.709		0.321

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.367
r_dihedral_angle_6_deg	13.12
r_lrange_it	9.202
r_lrange_other	9.202
r_scangle_it	6.466
r_scangle_other	6.465
r_mcangle_it	6.021
r_mcangle_other	6.021
r_dihedral_angle_1_deg	5.87
r_dihedral_angle_2_deg	5.011
r_scbond_it	3.944
r_scbond_other	3.944
r_mcbond_it	3.682
r_mcbond_other	3.682
r_angle_refined_deg	1.105
r_symmetry_xyhbond_nbd_refined	0.554
r_angle_other_deg	0.393
r_xyhbond_nbd_other	0.325
r_nbd_refined	0.261
r_nbd_other	0.249
r_symmetry_nbd_other	0.205
r_symmetry_nbd_refined	0.202
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.168
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.049
r_ncsr_local_group_6	0.046
r_ncsr_local_group_4	0.042
r_ncsr_local_group_2	0.04
r_ncsr_local_group_5	0.038
r_ncsr_local_group_1	0.037
r_ncsr_local_group_3	0.036
r_ncsr_local_group_7	0.023
r_symmetry_xyhbond_nbd_other	0.021
r_ext_dist_refined_b	0.01
r_bond_refined_d	0.006
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	22022
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing