2RKN | pdb_00002rkn

X-ray structure of the self-defense and signaling protein DIR1 from Arabidopsis taliana

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	0.08M acetate buffer pH 6.0, 0.02M ZnSO4, 22% PEG 600 MME, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 28.655	α = 90
b = 48.217	β = 90
c = 54.406	γ = 90

Symmetry
Space Group	P 21 21 21

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	Mirrors	2006-04-04	M	MAD
2	1	x-ray	100	CCD	ADSC QUANTUM 210	Mirrors	2006-11-17	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.28230, 1.28310, 1.2770	ESRF	ID29
2	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.9330	ESRF	ID14-1

Data Collection

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.82	1.92	100

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	1.6	9.92	10412	10335	496	99.51	0.192	0.192	0.189	0.1941	0.252	0.2584	RANDOM	38.162

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			0.03		-0.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	49.507
r_dihedral_angle_3_deg	15.808
r_scangle_it	4.768
r_dihedral_angle_1_deg	4.667
r_scbond_it	3.109
r_mcangle_it	2.266
r_angle_refined_deg	2.229
r_mcbond_it	1.567
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	49.507
r_dihedral_angle_3_deg	15.808
r_scangle_it	4.768
r_dihedral_angle_1_deg	4.667
r_scbond_it	3.109
r_mcangle_it	2.266
r_angle_refined_deg	2.229
r_mcbond_it	1.567
r_nbtor_refined	0.328
r_symmetry_hbond_refined	0.313
r_nbd_refined	0.288
r_symmetry_vdw_refined	0.284
r_xyhbond_nbd_refined	0.224
r_symmetry_metal_ion_refined	0.215
r_chiral_restr	0.129
r_metal_ion_refined	0.08
r_bond_refined_d	0.02
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	557
Nucleic Acid Atoms
Solvent Atoms	124
Heterogen Atoms	63

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing
SOLOMON	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection

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.