3JTX

Crystal structure of Aminotransferase (NP_283882.1) from NEISSERIA MENINGITIDIS Z2491 at 1.91 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	20.0000% polyethylene glycol 8000, 0.2000M calcium acetate, 0.1M MES pH 6.0, Additive: 0.001M pyridoxal-5'-phosphate(PLP), NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.09

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.617	α = 90
b = 116.89	β = 90
c = 145.326	γ = 90

Symmetry
Space Group	C 2 2 21

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	2009-05-14	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97922,0.97936	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	1.91	29.311	98.8	0.059	11.55			74211		-3	22.33

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	1.91	1.98	98.8		0.418	2.2

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	MAD	THROUGHOUT	1.91	29.311	74182	3737	99.75	0.154	0.152	0.183	RANDOM	20.07

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]
0.95			0.17		-1.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.175
r_dihedral_angle_4_deg	20.903
r_dihedral_angle_3_deg	12.237
r_dihedral_angle_1_deg	5.736
r_scangle_it	2.83
r_scbond_it	1.742
r_angle_refined_deg	1.344
r_mcangle_it	1.09
r_angle_other_deg	0.894
r_mcbond_it	0.589

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.175
r_dihedral_angle_4_deg	20.903
r_dihedral_angle_3_deg	12.237
r_dihedral_angle_1_deg	5.736
r_scangle_it	2.83
r_scbond_it	1.742
r_angle_refined_deg	1.344
r_mcangle_it	1.09
r_angle_other_deg	0.894
r_mcbond_it	0.589
r_mcbond_other	0.149
r_chiral_restr	0.078
r_bond_refined_d	0.012
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	6175
Nucleic Acid Atoms
Solvent Atoms	680
Heterogen Atoms	87

Software

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.