8X88 | pdb_00008x88

The Crystal Structure of TNIK from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RA7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	2.4M Sodium malonate dibasic monohydrate,7

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.75	α = 90
b = 112.75	β = 90
c = 125.356	γ = 120

Symmetry
Space Group	P 31 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 PILATUS3 6M		2022-01-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.18071	CLSI	08ID-1

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	2.7	48.82	100	0.055	28.8	9.9		25806

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	2.7	2.83			1.106	2.3

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	2.7	45.535	25777	1226	99.961	0.201	0.1981	0.2	0.2561	0.26	80.368

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]
-0.406	-0.203		-0.406		1.318

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.92
r_lrange_it	13.659
r_lrange_other	13.658
r_dihedral_angle_6_deg	11.159
r_scangle_it	7.795
r_scangle_other	7.794
r_mcangle_other	7.461
r_mcangle_it	7.46
r_dihedral_angle_2_deg	7.083
r_dihedral_angle_1_deg	5.805
r_scbond_it	4.959
r_scbond_other	4.958
r_mcbond_it	4.855
r_mcbond_other	4.855
r_angle_refined_deg	0.984
r_angle_other_deg	0.347
r_nbd_refined	0.222
r_symmetry_nbd_other	0.194
r_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.177
r_nbd_other	0.141
r_symmetry_nbd_refined	0.13
r_symmetry_nbtor_other	0.075
r_symmetry_xyhbond_nbd_refined	0.066
r_chiral_restr	0.047
r_bond_refined_d	0.004
r_gen_planes_refined	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	4699
Nucleic Acid Atoms
Solvent Atoms	43
Heterogen Atoms

Software

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