3FY0 | pdb_00003fy0

Crystal structure of PAK1 kinase domain with ruthenium complex DW1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	277	0.1M HEPES pH 7.5, 1M NaCl, 25% PEG 10000, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.05	α = 90
b = 102.66	β = 90
c = 122.341	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		CCD	MARMOSAIC 300 mm CCD		2007-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B		APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.35	50	99.2	0.143	11.3	5.5	14267	14162

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.35	2.43	100		0.402	4	5.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.35	47.14	13625	13418	716	98.48	0.20451	0.20161	0.1972	0.26	0.2557	RANDOM	30.699

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			0.27		-0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.723
r_dihedral_angle_4_deg	20.38
r_dihedral_angle_3_deg	15.565
r_dihedral_angle_1_deg	5.987
r_scangle_it	2.407
r_mcangle_it	2.375
r_mcbond_it	1.531
r_scbond_it	1.521
r_angle_refined_deg	1.321
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.218
r_nbd_refined	0.201
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.155
r_chiral_restr	0.086
r_bond_refined_d	0.012
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2263
Nucleic Acid Atoms
Solvent Atoms	119
Heterogen Atoms	31

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling