1NO3

REFINED STRUCTURE OF SOYBEAN LIPOXYGENASE-3 WITH 4-NITROCATECHOL AT 2.15 ANGSTROM RESOLUTION

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BYT	PDB ENTRY 1BYT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.3	295	20% PEG 8000, citrate-phosphate buffer 0.05M, tris.HCl, 0.2% sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.33	46.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 112.905	α = 90
b = 137.531	β = 95.48
c = 61.88	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	295	IMAGE PLATE	RIGAKU RAXIS IV	Focusing mirrors	1997-11-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	2.15	40	0.988	0.079	13.7	2	50978	50343			34.02

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	2.15	2.23	0.993		0.346	2.14	2	5046

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1BYT	2.15	10	49989	47446	2543	99.08	0.1887	0.1887	0.1863	0.2326	RANDOM	26.82

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]
0.91		0.97	0.63		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.451
r_scangle_it	4.163
r_scbond_it	2.902
r_angle_refined_deg	1.979
r_mcangle_it	1.652
r_mcbond_it	0.929
r_symmetry_hbond_refined	0.298
r_xyhbond_nbd_refined	0.202
r_nbd_refined	0.161
r_symmetry_vdw_refined	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.451
r_scangle_it	4.163
r_scbond_it	2.902
r_angle_refined_deg	1.979
r_mcangle_it	1.652
r_mcbond_it	0.929
r_symmetry_hbond_refined	0.298
r_xyhbond_nbd_refined	0.202
r_nbd_refined	0.161
r_symmetry_vdw_refined	0.148
r_chiral_restr	0.13
r_bond_refined_d	0.016
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6799
Nucleic Acid Atoms
Solvent Atoms	494
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CCP4	phasing

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 R01GM157729.