9D4W | pdb_00009d4w

Structure of PAK1 in complex with compound 12

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	6.6	293	0.1 M Na-malonate buffer, pH 6.6 , 0.15 M DL-malic acid, 4% propanediol, and 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.67

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.792	α = 90
b = 81.432	β = 106.555
c = 65.622	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 EIGER X 9M		2021-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS-II BEAMLINE 17-ID-1	0.97932	NSLS-II	17-ID-1

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	2.218	29.677	96.6	0.997	9.6	5.6		30467

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	2.218	2.27			0.763	1.3

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	2.218	29.677	30449	1478	96.636	0.183	0.1807	0.1846	0.2318	0.2352	69.541

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]
-0.799		-0.451	0.676		0.332

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.154
r_dihedral_angle_6_deg	14.878
r_lrange_other	13.053
r_lrange_it	13.046
r_scangle_it	10.758
r_scangle_other	10.753
r_mcangle_other	8.351
r_mcangle_it	8.35
r_scbond_it	7.25
r_scbond_other	7.233
r_dihedral_angle_2_deg	6.7
r_dihedral_angle_1_deg	6.699
r_mcbond_other	5.839
r_mcbond_it	5.838
r_angle_refined_deg	1.741
r_angle_other_deg	0.576
r_nbd_refined	0.219
r_symmetry_nbd_other	0.203
r_nbtor_refined	0.185
r_nbd_other	0.177
r_xyhbond_nbd_refined	0.167
r_symmetry_nbd_refined	0.089
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.08
r_symmetry_xyhbond_nbd_other	0.069
r_symmetry_xyhbond_nbd_refined	0.044
r_bond_refined_d	0.008
r_chiral_restr_other	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	4383
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	50

Software

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