3QQM

Crystal structure of a Putative amino-acid aminotransferase (NP_104211.1) from Mesorhizobium loti at 2.30 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	277	0.200M NH4I, 20.00% PEG-3350, No Buffer pH 6.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 116.178	α = 90
b = 215.574	β = 90
c = 81.875	γ = 90

Symmetry
Space Group	P 21 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	MARMOSAIC 325 mm CCD	FLAT COLLIMATING MIRROR, TOROID FOCUSING MIRROR	2009-03-20	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)	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	2.3	29.683	98.6	0.084	8.97			91682		-3	32.589

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	2.3	2.38	96.2		0.428	1.8

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	2.3	29.683	91628	4592	99.63	0.1956	0.1932	0.2407	RANDOM	23.3535

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]
0.71			-0.37		-0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.577
r_dihedral_angle_3_deg	9.411
r_dihedral_angle_4_deg	8.541
r_dihedral_angle_1_deg	2.437
r_scangle_it	1.788
r_angle_refined_deg	1.461
r_scbond_it	1.056
r_angle_other_deg	0.803
r_mcangle_it	0.64
r_mcbond_it	0.329

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.577
r_dihedral_angle_3_deg	9.411
r_dihedral_angle_4_deg	8.541
r_dihedral_angle_1_deg	2.437
r_scangle_it	1.788
r_angle_refined_deg	1.461
r_scbond_it	1.056
r_angle_other_deg	0.803
r_mcangle_it	0.64
r_mcbond_it	0.329
r_mcbond_other	0.079
r_chiral_restr	0.077
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13129
Nucleic Acid Atoms
Solvent Atoms	773
Heterogen Atoms	247

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.