9D4V | pdb_00009d4v

Structure of PAK1 in complex with compound 7

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	7	293	0.2 M Na-malonate, pH 7.0, 0.15 M DL-malic acid, 4% propane-diol, and 16% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.21

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.727	α = 90
b = 80.824	β = 107.274
c = 65.857	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		2023-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.9792	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.84	59.9	99.4	0.055	0.063	0.029	0.998	10.1	4.4		54294

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.84	1.87	99.7		1.687	1.907	0.875	0.578	0.7	4.6

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)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.84	49.633	53968	3847	98.988	0.202	0.1968	0.2026	0.2687	0.269	RANDOM	65.625

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]
-0.112		0.048	0.123		-0.034

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	18.907
r_dihedral_angle_6_deg	16
r_lrange_it	15.349
r_lrange_other	15.343
r_scangle_it	13.951
r_scangle_other	13.919
r_dihedral_angle_2_deg	11.776
r_mcangle_other	11.667
r_mcangle_it	11.65
r_scbond_it	11.034
r_scbond_other	10.96
r_mcbond_it	9.517
r_mcbond_other	9.517
r_dihedral_angle_1_deg	7.819
r_angle_refined_deg	2.54
r_angle_other_deg	0.792
r_nbd_refined	0.231
r_symmetry_nbd_other	0.219
r_symmetry_xyhbond_nbd_refined	0.219
r_nbtor_refined	0.199
r_symmetry_nbd_refined	0.187
r_nbd_other	0.18
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.124
r_symmetry_nbtor_other	0.095
r_symmetry_xyhbond_nbd_other	0.02
r_bond_refined_d	0.017
r_gen_planes_refined	0.014
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4398
Nucleic Acid Atoms
Solvent Atoms	76
Heterogen Atoms	48

Software

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