2ODB

The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GRN	pdb entry 1GRN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.1M acetate, 2M (NH4)2SO4, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.44	64.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.366	α = 90
b = 162.366	β = 90
c = 45.968	γ = 120

Symmetry
Space Group	P 65 2 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	CCD	MARMOSAIC 225 mm CCD		2006-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	2.4	40.59	100	0.071	0.071				14484

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	2.4	2.53	100		0.502	0.502

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 (All)	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 entry 1GRN	2.4	40.59	13737	13737	732	99.97	0.20484	0.20484	0.2034	0.21	0.23184	0.23	RANDOM	47.158

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]
-4.96	-2.48		-4.96		7.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.341
r_dihedral_angle_4_deg	13.291
r_dihedral_angle_3_deg	13.071
r_dihedral_angle_1_deg	6.655
r_scangle_it	1.965
r_angle_refined_deg	1.466
r_scbond_it	1.284
r_angle_other_deg	0.92
r_mcangle_it	0.792
r_mcbond_it	0.496
r_symmetry_vdw_refined	0.247
r_symmetry_vdw_other	0.219
r_nbd_refined	0.201
r_nbd_other	0.182
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.144
r_metal_ion_refined	0.125
r_nbtor_other	0.086
r_mcbond_other	0.083
r_symmetry_hbond_refined	0.081
r_chiral_restr	0.078
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1625
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	49

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing