3ELE | pdb_00003ele

Crystal structure of Amino Transferase (RER070207001803) from Eubacterium rectale at 2.10 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	1.0000M LiCl, 20.0000% PEG-6000, 0.1M HEPES pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.564	α = 82.51
b = 68.387	β = 79.52
c = 98.112	γ = 75.68

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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2008-08-10	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97936,0.97917	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	2.1	29.881	97.6	0.069	0.069	9.121	2		92103			25.239

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	2.1	2.15	96.7		0.35	0.35	2.1	2	6769

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	2.1	29.881	92101	4610	97.57	0.175	0.173	0.18	0.222	0.23	RANDOM	36.74

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]
-1.47	0.48	0.22	-1.69	-1.15	3.14

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.234
r_dihedral_angle_4_deg	13.839
r_dihedral_angle_3_deg	11.051
r_scangle_it	3.922
r_dihedral_angle_1_deg	3.871
r_scbond_it	3.038
r_angle_refined_deg	1.618
r_mcangle_it	1.602
r_angle_other_deg	1.312
r_mcbond_it	0.982
r_nbd_refined	0.167
r_mcbond_other	0.163
r_symmetry_hbond_refined	0.161
r_nbtor_refined	0.156
r_symmetry_vdw_other	0.146
r_nbd_other	0.137
r_symmetry_vdw_refined	0.112
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.095
r_nbtor_other	0.072
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.003
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12432
Nucleic Acid Atoms
Solvent Atoms	772
Heterogen Atoms	114

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