8YGX | pdb_00008ygx

Structure of the PYK2 from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.2M MgCl2, 0.1M Bis-Tris pH5.5-5.9, 19-29% PEG3,350,1mM TCEP

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.27

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.253	α = 90
b = 94.514	β = 91.68
c = 42.668	γ = 90

Symmetry
Space Group	P 1 21 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 PILATUS 6M		2021-10-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.000000	SPring-8	BL45XU

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	42.686	95.1	0.181	5.5	3.5		18990

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	2.05			0.479

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	42.686	18983	880	95.062	0.209	0.2067	0.21	0.2703	0.28	25.084

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]
0.185		-0.39	0.141		-0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.188
r_dihedral_angle_3_deg	13.379
r_dihedral_angle_1_deg	5.793
r_lrange_it	5.01
r_lrange_other	4.772
r_dihedral_angle_2_deg	4.464
r_scangle_it	3.044
r_scangle_other	3.043
r_mcangle_other	2.369
r_mcangle_it	2.368
r_scbond_it	1.824
r_scbond_other	1.823
r_mcbond_it	1.447
r_mcbond_other	1.447
r_angle_refined_deg	1.116
r_angle_other_deg	0.392
r_nbd_refined	0.211
r_symmetry_nbd_other	0.18
r_nbtor_refined	0.177
r_symmetry_nbd_refined	0.176
r_xyhbond_nbd_refined	0.175
r_nbd_other	0.172
r_symmetry_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.055
r_gen_planes_refined	0.004
r_bond_refined_d	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2067
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms

Software

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