2J59 | pdb_00002j59

Crystal structure of the ARF1:ARHGAP21-ArfBD complex

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1J2I	PDB ENTRY 1J2I

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.8		15 % PEG5000 MME, 100 MM IMIDAZOLE PH 6.8, 150 MM NH4.SO4 OR LI2SO4, 10 MM MGCL2, 0.5 % DIOXANE, 5 % ETHYLENE GLYCOL

Crystal Properties
Matthews coefficient	Solvent content
3.32	62.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.636	α = 90
b = 132.136	β = 90.01
c = 146.283	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	CCD	MARRESEARCH		2006-03-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3		ESRF	ID14-3

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	2.1	50	98.4	0.09	14.6	3.8		155860		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	2.1	2.21	95.5		0.37	3.8

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 (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 1J2I	2.1	40	180555	19925	97.3	0.209	0.205	0.2	0.243	0.23	RANDOM	23.45

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]
0.54		0.06	0.7		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.57
r_dihedral_angle_4_deg	20.302
r_dihedral_angle_3_deg	13.656
r_dihedral_angle_1_deg	5.884
r_scangle_it	2.244
r_scbond_it	1.464
r_angle_refined_deg	1.203
r_mcangle_it	1.073
r_mcbond_it	0.637
r_nbtor_refined	0.298
r_symmetry_vdw_refined	0.207
r_nbd_refined	0.19
r_symmetry_hbond_refined	0.15
r_xyhbond_nbd_refined	0.142
r_chiral_restr	0.082
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	13577
Nucleic Acid Atoms
Solvent Atoms	1656
Heterogen Atoms	258

Software

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