9F3V | pdb_00009f3v

RIP2K kinase domain dimer with bound compound 37 (N399), a speific NOD1 pathway inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	Compound 37, in powder form was solubilized in DMSO at 5 mM concentration. One aliquot of protein at 1.14 mg/ml was thawed and mixed with 50 microM inhibitor and kept on ice for 10 minutes. The complex was than concentrated to 3.8 mg/ml. solutions containing 3.8 mg/ml of protein-inhibitor complex equilibrated against 0.1 M citric acid and 0.8 M sodium formate at pH 5.

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.824	α = 90
b = 90.75	β = 90
c = 137.976	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 PILATUS3 6M		2023-06-20	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)	Rrim I (All)	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	1.943	54.981	96.1	0.093	0.104	0.996	8	5.3		48396

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.943	1.976	95.5		2.848	3.171	0.393	0.4

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	1.943	54.981	48396	2454	93.84	0.222	0.2203	0.2297	0.2564	0.2652	57.567

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]
-1.722			3.057		-1.336

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.671
r_dihedral_angle_3_deg	14.331
r_lrange_it	9.651
r_lrange_other	9.643
r_dihedral_angle_2_deg	9.276
r_scangle_it	6.832
r_scangle_other	6.831
r_mcangle_it	5.99
r_mcangle_other	5.989
r_dihedral_angle_1_deg	5.912
r_scbond_it	4.17
r_scbond_other	4.169
r_mcbond_it	3.913
r_mcbond_other	3.913
r_angle_refined_deg	1.084
r_angle_other_deg	0.37
r_nbd_other	0.212
r_nbd_refined	0.209
r_symmetry_xyhbond_nbd_refined	0.195
r_symmetry_nbd_other	0.188
r_symmetry_nbd_refined	0.186
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.152
r_ncsr_local_group_1	0.106
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.055
r_symmetry_xyhbond_nbd_other	0.044
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4504
Nucleic Acid Atoms
Solvent Atoms	129
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
autoPROC	data reduction
autoPROC	data scaling