Experiment: 2EFH

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		nucloetide-free Ara7/AtVps9a which was solved by MAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	20% PEG3350, 200mM lithium citrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.24	45.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.466	α = 81.9
b = 58.606	β = 87.42
c = 68.974	γ = 72.75

Symmetry
Space Group	P 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	ADSC QUANTUM 315		2006-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.00000	SPring-8	BL41XU

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	2.1	100	93.2	0.051	0.051	12.5	1.9		47121	1	1	30.8

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	2.18	70.9		0.277	1.9	1.5

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	nucloetide-free Ara7/AtVps9a which was solved by MAD	2.1	68.36	44747	2374	92.79	0.21599	0.21369	0.21	0.259	0.26	RANDOM	34.821

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]
-0.8	0.49	-0.19	0.41	-0.14	0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.716
r_dihedral_angle_4_deg	20.342
r_dihedral_angle_3_deg	16.878
r_dihedral_angle_1_deg	5.498
r_scangle_it	2.561
r_scbond_it	1.551
r_angle_refined_deg	1.205
r_mcangle_it	1.152
r_mcbond_it	0.668
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.716
r_dihedral_angle_4_deg	20.342
r_dihedral_angle_3_deg	16.878
r_dihedral_angle_1_deg	5.498
r_scangle_it	2.561
r_scbond_it	1.551
r_angle_refined_deg	1.205
r_mcangle_it	1.152
r_mcbond_it	0.668
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.232
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.149
r_symmetry_hbond_refined	0.103
r_chiral_restr	0.091
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6266
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	56

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.