8C12 | pdb_00008c12

Identification of an intermediate activation state of PAK5 reveals a novel mechanism of kinase inhibition.

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2F57
experimental model	PDB	6YXW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	291	0.12 M Alcohols (0.2 M 1,6-Hexanediol, 0.2 M 1-Butanol, 0.2 M 1,2_Propanediol, 0.2 M 2-Propanol, 0.2 M 1,4-Butanediol, 0.2 M 1,3-Propanediol), 0.1 M Buffer System 2 (1.0 M Sodium HEPES, MOPS) pH 7.5, 37.5% precipitant (M1K3350)

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.355	α = 90
b = 58.313	β = 90
c = 129.472	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 XE 16M		2022-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9795	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.549	53.17	100	0.056	0.059	0.016	0.999	16.3	13.4		64001			28.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	97.8		2.812	2.922	0.783	0.577		13.4

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	1.549	53.169	63911	3170	99.872	0.199	0.1972	0.21	0.2341	0.24	40.435

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]
-1.668			3.318		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.716
r_dihedral_angle_3_deg	13.153
r_dihedral_angle_4_deg	13.029
r_dihedral_angle_1_deg	6.109
r_lrange_it	2.945
r_lrange_other	2.812
r_scangle_it	2.043
r_scangle_other	2.043
r_mcangle_it	1.997
r_mcangle_other	1.997
r_scbond_it	1.569
r_scbond_other	1.569
r_mcbond_it	1.483
r_mcbond_other	1.482
r_angle_refined_deg	1.208
r_angle_other_deg	1.165
r_rigid_bond_restr	0.664
r_nbd_refined	0.179
r_nbd_other	0.178
r_symmetry_nbd_other	0.171
r_symmetry_xyhbond_nbd_refined	0.166
r_nbtor_refined	0.149
r_symmetry_nbd_refined	0.132
r_xyhbond_nbd_refined	0.128
r_symmetry_nbtor_other	0.073
r_symmetry_xyhbond_nbd_other	0.055
r_chiral_restr	0.052
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	3047
Nucleic Acid Atoms
Solvent Atoms	195
Heterogen Atoms

Software

Software
Software Name	Purpose
DIALS	data reduction
PHASER	phasing
REFMAC	refinement
Coot	model building