9D50 | pdb_00009d50

Structure of PAK1 in complex with compound 24

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5DEW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	100 mM malonate pH 6.6, 150 mM malic acid, 19% PEG 3350, 4% 1,2-propanediol

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.267	α = 90
b = 80.951	β = 108.797
c = 65.634	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		2022-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97918	ALBA	XALOC

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	1.898	54.213	99.8	0.997	9.8	5.51		44800

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.898	1.93			0.564	1.7

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	1.898	54.213	44799	2331	99.791	0.186	0.1839	0.1901	0.2299	0.2342	47.126

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]
0.037		0.106	0.051		-0.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.271
r_dihedral_angle_3_deg	13.414
r_dihedral_angle_2_deg	9.679
r_lrange_other	7.774
r_lrange_it	7.768
r_dihedral_angle_1_deg	6.589
r_scangle_it	6.297
r_scangle_other	6.296
r_mcangle_it	4.333
r_mcangle_other	4.332
r_scbond_it	4.231
r_scbond_other	4.23
r_mcbond_it	3.117
r_mcbond_other	3.113
r_angle_refined_deg	1.716
r_angle_other_deg	0.556
r_nbd_other	0.228
r_nbd_refined	0.209
r_symmetry_nbd_other	0.191
r_xyhbond_nbd_refined	0.181
r_symmetry_nbd_refined	0.18
r_symmetry_xyhbond_nbd_refined	0.179
r_nbtor_refined	0.176
r_chiral_restr	0.087
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.007
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	4339
Nucleic Acid Atoms
Solvent Atoms	179
Heterogen Atoms	60

Software

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