3RDE | pdb_00003rde

Crystal structure of the catalytic domain of porcine leukocyte 12-lipoxygenase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P0M	PDB ENTRY 2P0M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	protein 6 mg/mL incubated with the solid OPP inhibitor for 16 hours, then further concentrated to 11~12 mg/mL in 10 mM Tris HCl, 1 mM TCEP, pH 7.4 buffer. reservoir solution: 0.1 M MES pH 6.5, 5%-10% PEG-20,000, 20% glycerol against 1 mL well solution of 0.1 M MES, 5%-10% PEG-20,000, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 83.45	α = 90
b = 181.54	β = 92.86
c = 91.61	γ = 90

Symmetry
Space Group	P 1 21 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 300 mm CCD		2011-02-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.0781	APS	21-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.89	48.968	99.5	0.098	9	3.6	214779	214779

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	1.89	1.99	98.3		0.284	0.284	2.4	3.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2P0M	1.892	48.968	214717	6468	99.4	0.17323	0.17195	0.18	0.21447	0.22	RANDOM	17.665

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]
0.13		0.05	-0.17		0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.678
r_dihedral_angle_4_deg	22.438
r_dihedral_angle_3_deg	14
r_dihedral_angle_1_deg	6.097
r_scangle_it	5.304
r_angle_other_deg	4.113
r_scbond_it	3.475
r_mcangle_it	2.244
r_angle_refined_deg	1.974
r_mcbond_it	1.337
r_chiral_restr	0.137
r_bond_refined_d	0.026
r_gen_planes_other	0.017
r_gen_planes_refined	0.012
r_bond_other_d
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17580
Nucleic Acid Atoms
Solvent Atoms	1274
Heterogen Atoms	110

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction