3LVR

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

X-RAY DIFFRACTION

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); Crystals were then soaked in 30mM CaCl2 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 146.45	α = 90
b = 146.45	β = 90
c = 49.62	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		2009-04-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.3838	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	29.46	99.7	0.101	0.08	19	5.85	8310	8310	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	99.5		0.575	0.676	3.5	5.8	1657

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 3LVQ	3.38	29.46	8294	437	100	0.21095	0.20746	0.28129	RANDOM	125.397

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]
-6.75	-3.38		-6.75		10.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.465
r_dihedral_angle_3_deg	17.901
r_dihedral_angle_4_deg	13.86
r_dihedral_angle_1_deg	5.473
r_angle_refined_deg	1.058
r_scangle_it	0.813
r_scbond_it	0.446
r_mcangle_it	0.405
r_nbtor_refined	0.299
r_mcbond_it	0.223

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.465
r_dihedral_angle_3_deg	17.901
r_dihedral_angle_4_deg	13.86
r_dihedral_angle_1_deg	5.473
r_angle_refined_deg	1.058
r_scangle_it	0.813
r_scbond_it	0.446
r_mcangle_it	0.405
r_nbtor_refined	0.299
r_mcbond_it	0.223
r_nbd_refined	0.201
r_symmetry_vdw_refined	0.195
r_xyhbond_nbd_refined	0.137
r_metal_ion_refined	0.113
r_chiral_restr	0.076
r_bond_refined_d	0.006
r_gen_planes_refined	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3257
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	35

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.