9D4X | pdb_00009d4x

Structure of PAK1 in complex with compound 16

X-RAY DIFFRACTION

---

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	8	293	0.1 M Na-malonate buffer, pH 6.8 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.43	49.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.306	α = 90
b = 80.946	β = 106.61
c = 65.883	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		2022-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97926	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	1.847	60.738	93.2	0.997	10.9	5.3		50948

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	1.847	1.879			0.603

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	1.847	60.738	50878	2562	93.023	0.19	0.1879	0.1957	0.2266	0.2283	58.183

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]
1.895		2.311	-1.047		-1.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.241
r_dihedral_angle_3_deg	14.896
r_lrange_it	10.519
r_lrange_other	10.519
r_scangle_it	8.202
r_scangle_other	8.201
r_dihedral_angle_2_deg	7.585
r_dihedral_angle_1_deg	6.381
r_mcangle_it	6.045
r_mcangle_other	6.044
r_scbond_it	5.339
r_scbond_other	5.338
r_mcbond_it	4.287
r_mcbond_other	4.284
r_angle_refined_deg	1.68
r_angle_other_deg	0.56
r_symmetry_xyhbond_nbd_refined	0.438
r_nbd_refined	0.221
r_symmetry_nbd_refined	0.205
r_symmetry_nbd_other	0.198
r_nbd_other	0.196
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.148
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.08
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	4370
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	62

Software

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