9D52 | pdb_00009d52

Structure of PAK4 in complex with compound 18

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J0I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1 M HEPES pH 7.5, 4% (v/v) PEG 8000

Crystal Properties
Matthews coefficient	Solvent content
2.75	55.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.642	α = 90
b = 62.642	β = 90
c = 184.886	γ = 90

Symmetry
Space Group	P 41 21 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 PILATUS 6M		2021-12-15	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	2.449	44.334	99.4	0.999	13.1	9.7		14318

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	2.449	2.46			0.515	1

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	2.449	44.334	14291	720	99.714	0.205	0.201	0.2058	0.2872	0.2873	70.203

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]
0.253			0.253		-0.506

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.359
r_dihedral_angle_6_deg	15.113
r_lrange_other	10.54
r_lrange_it	10.539
r_scangle_it	8.919
r_scangle_other	8.916
r_dihedral_angle_1_deg	7.971
r_mcangle_it	7.768
r_mcangle_other	7.766
r_dihedral_angle_2_deg	7.036
r_scbond_it	6.69
r_scbond_other	6.688
r_mcbond_it	6.031
r_mcbond_other	6.022
r_angle_refined_deg	2.514
r_angle_other_deg	0.795
r_nbd_other	0.252
r_nbd_refined	0.238
r_symmetry_nbd_other	0.217
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.167
r_chiral_restr	0.116
r_symmetry_nbtor_other	0.092
r_symmetry_xyhbond_nbd_other	0.086
r_symmetry_nbd_refined	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2289
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms	39

Software

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