4EQC | pdb_00004eqc

Crystal structure of PAK1 kinase domain in complex with FRAX597 inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FXZ	PDB ID 3FXZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	0.1 M HEPES, 1 M NaCl, 25% PEG 3350, 10 mM DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.4	48.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.494	α = 90
b = 103.026	β = 90
c = 122.35	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	RIGAKU SATURN 944+		2012-02-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	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	50	99.4	0.168	0.157	8	4.8	22221	22088

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.07	100		0.597	0.545	2.1	4.6	2189

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 3FXZ	2.01	30.53	21089	20927	1130	99.23	0.19798	0.19505	0.1928	0.25317	0.243	RANDOM	26.144

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]
-0.08			0.11		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.305
r_dihedral_angle_4_deg	25.561
r_dihedral_angle_3_deg	15.959
r_dihedral_angle_1_deg	7.882
r_scangle_it	3.935
r_scbond_it	2.627
r_angle_refined_deg	1.856
r_mcangle_it	1.597
r_mcbond_it	1.039
r_nbtor_refined	0.308
r_symmetry_hbond_refined	0.244
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.198
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2308
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	41

Software

Software
Software Name	Purpose
HKL-3000	data collection
PHASER	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling