3FHM | pdb_00003fhm

Crystal structure of the CBS-domain containing protein ATU1752 from Agrobacterium tumefaciens

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RC3	model of protein made from 3rc3 using MrBUMP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	295	0.1 M Tris 8.0, 0.2 M LiSO4, 30% PEG 4K plus 0.015 mg/ml V8 protease. Cryoprotected with Paratone-N oil, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 53.247	α = 115.21
b = 58.075	β = 106.15
c = 59.056	γ = 94.94

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	SBC-2	mirrors	2008-06-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.9794	APS	19-ID

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	2.4	30.37	81.7	0.067	18.55	4.5	24264	19824			47.9

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	2.4	2.44	11.6		0.545	1.1	2.1	143

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	model of protein made from 3rc3 using MrBUMP	2.7	30.37	14238	783	91.56	0.19887	0.19536	0.23	0.26164	0.28	RANDOM	33.886

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	0.02	0.02	-0.08	-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.903
r_dihedral_angle_4_deg	24.07
r_dihedral_angle_3_deg	22.661
r_dihedral_angle_1_deg	6.697
r_angle_refined_deg	2.251
r_symmetry_vdw_refined	0.342
r_nbtor_refined	0.313
r_nbd_refined	0.237
r_symmetry_hbond_refined	0.188
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.146
r_bond_refined_d	0.021
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3829
Nucleic Acid Atoms
Solvent Atoms	47
Heterogen Atoms	288

Software

Software
Software Name	Purpose
HKL-3000	data collection
MrBUMP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling