1S9D | pdb_00001s9d

ARF1[DELTA 1-17]-GDP-MG IN COMPLEX WITH BREFELDIN A AND A SEC7 DOMAIN

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1RRG	PDB ENTRY 1RRG and coordinates of arf1[D1-17]/Gea2-Sec7 (Goldberg, J., (1998) Cell 95(2): 237-48)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	289	29% PEG 3350, 40MM NH4CL, 40MM POTASSIUM FORMATE, 100MM TRIS, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.73	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 111.462	α = 90
b = 111.462	β = 90
c = 74.534	γ = 90

Symmetry
Space Group	P 41 21 2

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	mirrors	2003-04-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.980	ESRF	BM30A

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	1.8	30	98.1	0.05	26.2	12	43814	43814			22.76

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	1.8	1.85	97.1		0.405	6.4	12.1	3319

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 (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 ENTRY 1RRG and coordinates of arf1[D1-17]/Gea2-Sec7 (Goldberg, J., (1998) Cell 95(2): 237-48)	1.8	29.88	43814	41588	2225	99.54	0.184	0.18397	0.18193	0.19	0.22148	0.22	RANDOM	19.91

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]
-1.95			-1.95		3.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.862
r_scangle_it	5.065
r_scbond_it	3.243
r_mcangle_it	2.081
r_angle_refined_deg	1.94
r_mcbond_it	1.233
r_angle_other_deg	0.999
r_symmetry_vdw_other	0.284
r_nbd_other	0.256
r_symmetry_vdw_refined	0.249
r_nbd_refined	0.226
r_xyhbond_nbd_refined	0.176
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.128
r_nbtor_other	0.09
r_bond_refined_d	0.025
r_gen_planes_refined	0.01
r_gen_planes_other	0.006
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2830
Nucleic Acid Atoms
Solvent Atoms	286
Heterogen Atoms	49

Software

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