8XN6 | pdb_00008xn6

The Crystal Structure of GSK3b from Biortus.

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	20% PEG 3350, 5% Glycerol, 20mM MgCl2, 100mM Hepes pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
3.36	63.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.694	α = 90
b = 85.429	β = 90
c = 178.091	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 EIGER X 16M		2023-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953725	Australian Synchrotron	MX2

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	2.4	48.75	99.8	0.086	15.8	7.9		50034

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	2.4	2.48			1.039

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	2.4	42.751	50034	2516	99.763	0.194	0.1917	0.2	0.2424	0.24	59.962

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]
1.789			3.097		-4.885

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.186
r_dihedral_angle_4_deg	14.453
r_dihedral_angle_3_deg	13.101
r_lrange_other	10.124
r_lrange_it	10.123
r_dihedral_angle_1_deg	6.158
r_scangle_it	4.945
r_scangle_other	4.944
r_mcangle_it	4.922
r_mcangle_other	4.922
r_scbond_it	3.003
r_scbond_other	3.002
r_mcbond_it	2.931
r_mcbond_other	2.93
r_angle_refined_deg	1.209
r_angle_other_deg	1.087
r_nbd_refined	0.189
r_symmetry_xyhbond_nbd_refined	0.171
r_symmetry_nbd_other	0.164
r_nbtor_refined	0.158
r_xyhbond_nbd_refined	0.134
r_nbd_other	0.129
r_symmetry_nbtor_other	0.071
r_symmetry_nbd_refined	0.066
r_chiral_restr	0.051
r_chiral_restr_other	0.033
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	5676
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	157

Software

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