1R8S | pdb_00001r8s

ARF1[DELTA1-17]-GDP IN COMPLEX WITH A SEC7 DOMAIN CARRYING THE MUTATION OF THE CATALYTIC GLUTAMATE TO LYSINE

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1R8R	PDB ENTRY 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	289	1.88M Ammonium Sulfate, 100mM MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 104.018	α = 90
b = 104.018	β = 90
c = 69.277	γ = 120

Symmetry
Space Group	P 32 2 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					M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.931	ESRF	ID14-3

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.46	30		0.059	26.6	16		75051			18.35

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.46	1.47	97		0.462	5.9	12.1

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 (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 1R8R and crystal structure of the Arf1[D1-17]/Gea2-Sec7 complex (Goldberg, J., (1998) Cell 95(2):237-48)	1.46	28.87	75051	71299	3744	99.91	0.15941	0.15885	0.16	0.1698	0.17	RANDOM	12.525

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]
-0.05	-0.02		-0.05		0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.153
r_scangle_it	4.08
r_scbond_it	2.529
r_mcangle_it	1.68
r_angle_refined_deg	1.421
r_mcbond_it	0.881
r_angle_other_deg	0.87
r_symmetry_vdw_refined	0.56
r_symmetry_vdw_other	0.31
r_nbd_other	0.246
r_symmetry_hbond_refined	0.222
r_nbd_refined	0.218
r_xyhbond_nbd_refined	0.143
r_chiral_restr	0.086
r_nbtor_other	0.085
r_gen_planes_other	0.022
r_bond_other_d	0.018
r_bond_refined_d	0.015
r_gen_planes_refined	0.013
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2806
Nucleic Acid Atoms
Solvent Atoms	350
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling
CCP4	phasing