8QK4 | pdb_00008qk4

Dehydratase domain (PksJ DH1) from the bacillaene trans-AT PKS

X-RAY DIFFRACTION

---

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		293	22% PEG 3350 and 0.3 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.33

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.905	α = 90
b = 84.79	β = 90
c = 131.938	γ = 90

Symmetry
Space Group	P 21 21 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 EIGER X 16M		2022-07-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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	1.9	49.104	99.95	0.998	10.09	13.3		47606			27.8

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	1.9	1.97			0.975

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	1.9	49.104	47606	2247	99.977	0.178	0.1761	0.1864	0.2163	0.2239	32.718

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]
1.916			-1.625		-0.291

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.973
r_dihedral_angle_3_deg	13.721
r_lrange_it	8.626
r_lrange_other	8.594
r_dihedral_angle_1_deg	7.021
r_scangle_it	6.542
r_scangle_other	6.541
r_dihedral_angle_2_deg	6.368
r_mcangle_it	4.881
r_mcangle_other	4.88
r_scbond_it	4.11
r_scbond_other	4.109
r_mcbond_other	3.237
r_mcbond_it	3.236
r_angle_refined_deg	1.361
r_angle_other_deg	0.468
r_nbd_other	0.255
r_symmetry_nbd_refined	0.237
r_symmetry_xyhbond_nbd_refined	0.207
r_nbd_refined	0.204
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.173
r_xyhbond_nbd_refined	0.147
r_symmetry_nbtor_other	0.083
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4315
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms	33

Software

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