3DXO | pdb_00003dxo

CRYSTAL STRUCTURE OF A PUTATIVE ISOMERASE OF THE SNOAL-LIKE FAMILY (ATU_0744) FROM AGROBACTERIUM TUMEFACIENS STR. C58 AT 2.70 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	277	5.0000% PEG-6000, 0.1M Citrate pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.63	66.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.57	α = 90
b = 119.57	β = 90
c = 94.49	γ = 120

Symmetry
Space Group	P 61 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-06-27	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97968,0.97946	SSRL	BL9-2

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	2.7	28.724	97.6	0.113	7.04			11229		-3	49.301

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	2.7	2.8	97.8		0.454	1.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	MAD	THROUGHOUT	2.7	28.724	11216	542	98.41	0.233	0.231	0.23	0.262	0.27	RANDOM	23.437

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]
0.3	0.15		0.3		-0.44

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.058
r_dihedral_angle_4_deg	14.457
r_dihedral_angle_3_deg	13.911
r_dihedral_angle_1_deg	3.398
r_angle_refined_deg	1.652
r_scangle_it	1.301
r_mcangle_it	1.061
r_angle_other_deg	1.013
r_scbond_it	0.831
r_mcbond_it	0.772
r_symmetry_vdw_other	0.299
r_symmetry_vdw_refined	0.234
r_mcbond_other	0.227
r_nbd_refined	0.222
r_nbd_other	0.206
r_symmetry_hbond_refined	0.201
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.156
r_nbtor_other	0.093
r_chiral_restr	0.089
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.004
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1828
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing