3BB3

Crystal structure of Toc33 from Arabidopsis thaliana in complex with GDP and Mg2+

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	292	24% PEG1500, 20% Glycerol, pH7.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.617	α = 90
b = 121.617	β = 90
c = 42.769	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	ADSC QUANTUM 315		2006-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	1.0723	ESRF	ID23-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.9	29	99.3	0.081	14.4	6.1	7288	7234	-4	-3	82

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	2.94	3.04	97.9		0.466	1.9	4.2	702

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 1H65	2.94	25	6866	335	99.52	0.22006	0.218	0.26196	RANDOM	104.928

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]
-2.14			-2.14		4.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.329
r_dihedral_angle_3_deg	21.593
r_dihedral_angle_4_deg	17.793
r_dihedral_angle_1_deg	7.561
r_scangle_it	3.118
r_angle_refined_deg	2.057
r_scbond_it	1.99
r_mcangle_it	1.379
r_mcbond_it	0.85
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.329
r_dihedral_angle_3_deg	21.593
r_dihedral_angle_4_deg	17.793
r_dihedral_angle_1_deg	7.561
r_scangle_it	3.118
r_angle_refined_deg	2.057
r_scbond_it	1.99
r_mcangle_it	1.379
r_mcbond_it	0.85
r_nbtor_refined	0.301
r_symmetry_vdw_refined	0.268
r_nbd_refined	0.249
r_symmetry_hbond_refined	0.245
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.121
r_bond_refined_d	0.02
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1894
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	29

Software

Software
Software Name	Purpose
REFMAC	refinement
DNA	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 R01GM133198.