3BB4 | pdb_00003bb4

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

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H65	PDB ENTRY 1H65

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	296	22% PEG1500, 15% glycerol, pH7.4, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.567	α = 90
b = 121.567	β = 90
c = 42.879	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		2006-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.9746	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	2.84	25	99.6	0.085	15.39	5.8	7834	7827	-4	-3	69.8

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	2.84	2.94	100		0.486	2.2	6	748

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	PDB ENTRY 1H65	2.85	25	7461	366	98.53	0.22082	0.21802	0.19	0.27663	0.25	RANDOM	69.779

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]
-0.29			-0.29		0.58

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.202
r_dihedral_angle_4_deg	26.122
r_dihedral_angle_3_deg	21.698
r_dihedral_angle_1_deg	9.626
r_scangle_it	2.961
r_angle_refined_deg	2.073
r_scbond_it	1.916
r_angle_other_deg	1.359
r_mcangle_it	1.325
r_mcbond_it	1.144
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.241
r_nbd_other	0.219
r_symmetry_vdw_other	0.193
r_symmetry_hbond_refined	0.189
r_nbtor_refined	0.181
r_xyhbond_nbd_refined	0.175
r_chiral_restr	0.103
r_mcbond_other	0.089
r_nbtor_other	0.086
r_bond_refined_d	0.02
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1885
Nucleic Acid Atoms
Solvent Atoms	27
Heterogen Atoms	33

Software

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