3LVQ | pdb_00003lvq

The crystal structure of ASAP3 in complex with Arf6 in transition state

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B0O	PDB ENTRIES 2B0o and 2J5X
experimental model	PDB	2J5X	PDB ENTRIES 2B0o and 2J5X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	13% PEG 8000, 150mM Magnesium Acetate, 100mM MOPS(pH 7.5), VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.79	55.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.29	α = 90
b = 146.29	β = 90
c = 49.52	γ = 120

Symmetry
Space Group	P 62

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		2009-02-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.98	SLS	X06SA

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	3.38	29.42	99.7	0.066	0.079	22.52	9.25		8700	1	1

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)
	3.38	3.5	99.8		0.339	0.55	4.94	9.45	847

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 (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 ENTRIES 2B0o and 2J5X	3.38	29.42	8263	435	100	0.2207	0.2207	0.21881	0.2338	0.2568	0.2801	RANDOM	136.436

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]
-5.06	-2.53		-5.06		7.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.681
r_dihedral_angle_3_deg	18.641
r_dihedral_angle_4_deg	16.472
r_dihedral_angle_1_deg	5.63
r_angle_refined_deg	1.146
r_nbtor_refined	0.3
r_symmetry_vdw_refined	0.217
r_nbd_refined	0.21
r_xyhbond_nbd_refined	0.19
r_symmetry_hbond_refined	0.115
r_chiral_restr	0.082
r_metal_ion_refined	0.059
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3262
Nucleic Acid Atoms
Solvent Atoms	5
Heterogen Atoms	35

Software

Software
Software Name	Purpose
ProDC	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling