9HHY | pdb_00009hhy

Crystal Structure of the Coxiella burnetii 2-methylisocitrate lyase Bound to Inhibitor Isocitric Acid

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	MICROBATCH		292	Clear Strategy I D7: 0.3 M sodium acetate trihydrate, 0.1 M sodium cacodylate pH 6.5, 8% w/v PEG 20,000, 8% v/v PEG 500 MME

Crystal Properties
Matthews coefficient	Solvent content
2.56	52.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.785	α = 90
b = 115.55	β = 92.34
c = 195.241	γ = 90

Symmetry
Space Group	P 1 21 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		2022-12-13	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)	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	2.33	59.24	99.98	0.9945	8.29	7.04		177721

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	2.33	2.37			0.2991

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	2.33	59.24	168617	8841	99.83	0.21657	0.214	0.214	0.26523	0.2653	RANDOM	68.925

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]
2.57		1.57	-1.87		-0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.402
r_long_range_B_refined	21.983
r_mcangle_it	18.71
r_dihedral_angle_4_deg	17.295
r_scbond_it	15.816
r_dihedral_angle_3_deg	14.783
r_mcbond_it	14.276
r_dihedral_angle_1_deg	6.113
r_angle_refined_deg	1.195
r_chiral_restr	0.096
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26526
Nucleic Acid Atoms
Solvent Atoms	881
Heterogen Atoms	326

Software

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