8ZML | pdb_00008zml

Structure of TNIK with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5D7A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.2 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 20% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.889	α = 90
b = 89.595	β = 90
c = 97.577	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 EIGER2 R 4M		2024-04-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.97918	SSRF	BL02U1

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	2.489	65.995	99.9	0.999	17.2	9.2		25206

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	2.489	2.59			0.777

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	2.489	65.995	25156	1315	99.885	0.259	0.2556	0.257	0.3263	0.3232	64.798

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]
1.798			2.347		-4.145

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.605
r_dihedral_angle_3_deg	14.16
r_dihedral_angle_4_deg	13.236
r_dihedral_angle_1_deg	5.3
r_lrange_it	4.509
r_lrange_other	4.485
r_mcangle_it	2.331
r_mcangle_other	2.331
r_scangle_it	1.439
r_scangle_other	1.439
r_mcbond_other	1.259
r_mcbond_it	1.258
r_angle_refined_deg	1.177
r_angle_other_deg	0.985
r_scbond_it	0.726
r_scbond_other	0.726
r_nbd_refined	0.155
r_symmetry_nbd_refined	0.155
r_symmetry_nbd_other	0.15
r_nbtor_refined	0.143
r_xyhbond_nbd_refined	0.124
r_nbd_other	0.117
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_xyhbond_nbd_other	0.088
r_symmetry_nbtor_other	0.071
r_chiral_restr	0.033
r_bond_refined_d	0.002
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4843
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	82

Software

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