9WS6 | pdb_00009ws6

Crystal structure of AMP-PNP-bound PAK2 kinase domain containing D368N mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3Q52

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		291	0.1 M HEPES pH 7.0, 25% PEG 6000, 0.2 M MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.71

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.938	α = 90
b = 67.053	β = 91.055
c = 183.319	γ = 90

Symmetry
Space Group	C 1 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 R 200K-A		2022-07-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	50	95.3	0.084	0.997	19.8	7.6		86810

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07			0.769	0.543	1.9

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	22.699	86802	4305	90.503	0.196	0.1948	0.1988	0.2284	0.2304	48.7

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]
-7.856		1.873	-1.019		8.876

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.527
r_dihedral_angle_3_deg	14.403
r_lrange_other	11.371
r_lrange_it	11.363
r_scangle_it	7.703
r_scangle_other	7.702
r_dihedral_angle_1_deg	6.926
r_mcangle_it	6.922
r_mcangle_other	6.922
r_dihedral_angle_2_deg	6.118
r_scbond_it	5.328
r_scbond_other	5.322
r_mcbond_it	4.916
r_mcbond_other	4.916
r_angle_refined_deg	1.575
r_angle_other_deg	0.539
r_nbd_refined	0.195
r_symmetry_nbd_other	0.193
r_nbd_other	0.191
r_nbtor_refined	0.176
r_symmetry_nbd_refined	0.147
r_symmetry_xyhbond_nbd_refined	0.132
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.082
r_symmetry_nbtor_other	0.078
r_dihedral_angle_other_2_deg	0.02
r_chiral_restr_other	0.016
r_bond_refined_d	0.008
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9317
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	70

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing