2W83

Crystal structure of the ARF6 GTPase in complex with a specific effector, JIP4

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J5X	PDB ENTRY 2J5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				2.0 M AMONIUM SULFATE, 0.1 M HEPES PH 7.5, 0.2 M NACL, 2 MM MGCL2, 6 % MPD

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 137.27	α = 90
b = 137.27	β = 90
c = 165.03	γ = 120

Symmetry
Space Group	P 62 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	287	IMAGE PLATE	MAR555 FLAT PANEL		2008-04-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SOLEIL BEAMLINE PROXIMA 1		SOLEIL	PROXIMA 1

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	1.93	35	99.9	0.06	8	12.8		62165		2

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	1.93	2.03	98.2		0.4	2.1	11.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2J5X	1.93	118.68	62165	6987	99.9	0.217	0.214	0.238	RANDOM	30.43

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]
1.03	0.52		1.03		-1.55

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.731
r_dihedral_angle_3_deg	15.539
r_dihedral_angle_4_deg	15.156
r_dihedral_angle_1_deg	5.367
r_scangle_it	2.462
r_scbond_it	1.541
r_angle_refined_deg	1.17
r_mcangle_it	1.104
r_mcbond_it	0.686
r_symmetry_hbond_refined	0.335
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.258
r_nbd_refined	0.19
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.08
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4931
Nucleic Acid Atoms
Solvent Atoms	274
Heterogen Atoms	141

Software

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