9WS3 | pdb_00009ws3

Crystal structure of phosphorylated PAK2 kinase domain containing K278R 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 MES pH 6.5, 1.1 M ammonium tartrate, 0.2 M guanidine hydrochloride

Crystal Properties
Matthews coefficient	Solvent content
3.46	64.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.975	α = 90
b = 102.975	β = 90
c = 157.686	γ = 120

Symmetry
Space Group	P 63 2 2

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		2021-04-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54187

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	1.85	34	98.9	0.999	24	17.2		42174

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	1.85	1.89			0.798	0.843	2.2

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	1.85	29.552	42167	2157	98.468	0.189	0.1875	0.1973	0.2088	0.2148	32.657

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]
0.096	0.048		0.096		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.231
r_dihedral_angle_3_deg	12.983
r_lrange_it	9.034
r_lrange_other	8.853
r_scangle_other	7.134
r_scangle_it	7.13
r_dihedral_angle_1_deg	5.839
r_dihedral_angle_2_deg	5.141
r_scbond_it	4.715
r_scbond_other	4.713
r_mcangle_it	4.352
r_mcangle_other	4.351
r_mcbond_it	3.294
r_mcbond_other	3.29
r_angle_refined_deg	1.643
r_angle_other_deg	0.571
r_symmetry_nbd_refined	0.218
r_nbd_refined	0.214
r_dihedral_angle_other_2_deg	0.21
r_symmetry_nbd_other	0.193
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.169
r_symmetry_xyhbond_nbd_refined	0.148
r_nbd_other	0.114
r_chiral_restr	0.089
r_symmetry_nbtor_other	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2356
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms	6

Software

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