9I2P | pdb_00009i2p

Crystal structure of Listeria monocytogenes ChiA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q8Y619-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	292	10% (w/v) PEG 4000, 20% (w/v) glycerol, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM (RS)-1,2-propanediol, 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol, 100 mM 2-(N-morpholino) ethane sulfonic acid (MES), 100 mM imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.041	α = 94.308
b = 59.146	β = 110.69
c = 67.609	γ = 111.596

Symmetry
Space Group	P 1

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		2022-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95374	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.95	45.67	93	0.123	5.1	2.6		48104

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.95	2	93.7		0.344		2.6

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	1.95	45.592	48104	2399	92.864	0.182	0.1798	0.1901	0.2256	0.2314	18.532

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]
2.288	0.911	-0.467	1.97	-0.83	-2.881

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.822
r_dihedral_angle_3_deg	12.745
r_lrange_it	9.673
r_lrange_other	9.673
r_scangle_it	8.254
r_scangle_other	8.253
r_dihedral_angle_2_deg	7.409
r_dihedral_angle_1_deg	6.29
r_scbond_it	5.929
r_scbond_other	5.928
r_mcangle_other	4.713
r_mcangle_it	4.71
r_mcbond_it	3.642
r_mcbond_other	3.634
r_angle_refined_deg	1.804
r_angle_other_deg	0.601
r_nbd_refined	0.22
r_symmetry_nbd_other	0.203
r_symmetry_xyhbond_nbd_refined	0.198
r_nbd_other	0.188
r_nbtor_refined	0.186
r_xyhbond_nbd_refined	0.173
r_metal_ion_refined	0.125
r_symmetry_nbd_refined	0.1
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.084
r_ncsr_local_group_1	0.082
r_gen_planes_other	0.023
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4978
Nucleic Acid Atoms
Solvent Atoms	400
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing