3ES4

Crystal structure of Protein of unknown function (DUF861) with a RmlC-like cupin fold (17741406) from AGROBACTERIUM TUMEFACIENS str. C58 (Dupont) at 1.64 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	1.4M Na3Citrate, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.254	α = 90
b = 95.254	β = 90
c = 83.155	γ = 120

Symmetry
Space Group	H 3

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	2008-08-04	M	SINGLE WAVELENGTH

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

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.64	29.285	99.5	0.084	0.084	5.927	7.3		34348			17.626

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.64	1.68	94.3		0.371	0.371	2.1	5.1	2419

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	1.64	29.285	34317	1735	99.53	0.143	0.142	0.16	RANDOM	19.806

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		-0.45

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.322
r_dihedral_angle_4_deg	15.484
r_dihedral_angle_3_deg	12.408
r_dihedral_angle_1_deg	5.882
r_scangle_it	3.835
r_scbond_it	2.61
r_mcangle_it	2.532
r_mcbond_it	2.255
r_angle_refined_deg	1.605
r_angle_other_deg	0.865
r_mcbond_other	0.507
r_symmetry_vdw_other	0.317
r_symmetry_vdw_refined	0.313
r_nbd_other	0.213
r_nbd_refined	0.188
r_xyhbond_nbd_refined	0.18
r_nbtor_refined	0.177
r_symmetry_hbond_refined	0.143
r_chiral_restr	0.088
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1758
Nucleic Acid Atoms
Solvent Atoms	300
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SHARP	phasing