8GOD

Co-crystal structure of Human Protein-arginine deiminase type-4 (PAD4) with small molecule inhibitor JBI-589

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	299	0.1M HEPES pH 7.0, 5% (v/v) Tascimate pH 7.0, 20% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.456	α = 90
b = 60.879	β = 104.585
c = 127.097	γ = 90

Symmetry
Space Group	I 1 2 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 EIGER X 16M		2022-02-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1	0.97856	SOLEIL	PROXIMA 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	2.88	46.81	99.6	0.05	0.999	19.6	7		18844

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	2.88	3.04			0.54	0.98

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	4X8G	2.88	42.902	18829	940	99.372	0.209	0.2054	0.2726

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]
-3.363		0.687	14.049		-9.727

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.287
r_dihedral_angle_3_deg	15.441
r_dihedral_angle_4_deg	15.304
r_dihedral_angle_1_deg	7.514
r_lrange_it	6.919
r_lrange_other	6.918
r_mcangle_it	4.597
r_mcangle_other	4.597
r_scangle_it	4.245
r_scangle_other	4.245
r_mcbond_it	2.777
r_mcbond_other	2.775
r_scbond_it	2.549
r_scbond_other	2.549
r_angle_refined_deg	1.462
r_angle_other_deg	1.164
r_nbd_refined	0.22
r_nbd_other	0.204
r_symmetry_nbd_refined	0.19
r_symmetry_nbd_other	0.188
r_symmetry_xyhbond_nbd_other	0.178
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.075
r_chiral_restr_other	0.058
r_chiral_restr	0.052
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4429
Nucleic Acid Atoms
Solvent Atoms	4
Heterogen Atoms	36

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing