8YHW | pdb_00008yhw

The Crystal Structure of NF-kB-inducing Kinase (NIK) from Biortus

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4DN5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MMT pH9.0, 25% PEG1500

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.652	α = 90
b = 119.652	β = 90
c = 115.586	γ = 90

Symmetry
Space Group	P 41

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 S 6M		2023-10-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08B1-1	1.18079	CLSI	08B1-1

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	2.9	48.56	100	0.992	11.2	9.4		36217

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	2.9	3.03			0.709

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	2.9	48.56	36186	1628	99.967	0.196	0.194	0.2	0.2412	0.24	49.624

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]
0.255			0.255		-0.509

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	13.249
r_dihedral_angle_6_deg	12.801
r_lrange_it	7.652
r_lrange_other	7.65
r_dihedral_angle_1_deg	6.144
r_dihedral_angle_2_deg	5.004
r_scangle_it	4.861
r_scangle_other	4.86
r_mcangle_other	4.829
r_mcangle_it	4.828
r_mcbond_it	2.891
r_mcbond_other	2.878
r_scbond_it	2.877
r_scbond_other	2.877
r_angle_refined_deg	1.179
r_angle_other_deg	0.398
r_dihedral_angle_other_2_deg	0.319
r_nbd_refined	0.216
r_nbd_other	0.199
r_symmetry_nbd_other	0.185
r_symmetry_xyhbond_nbd_refined	0.174
r_nbtor_refined	0.171
r_symmetry_nbd_refined	0.153
r_xyhbond_nbd_refined	0.126
r_symmetry_nbtor_other	0.079
r_ncsr_local_group_2	0.066
r_symmetry_xyhbond_nbd_other	0.065
r_ncsr_local_group_4	0.063
r_ncsr_local_group_6	0.062
r_ncsr_local_group_3	0.061
r_ncsr_local_group_1	0.06
r_ncsr_local_group_5	0.059
r_chiral_restr	0.057
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	10356
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms	173

Software

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