3DY5 | pdb_00003dy5

Allene oxide synthase 8R-lipoxygenase from Plexaura homomalla

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2FNQ	PDB entries 2FNQ, 1U5U
experimental model	PDB	1U5U	PDB entries 2FNQ, 1U5U

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	295	The drops were prepared with 2:1:1 mixtures of protein (5 mg/mL in 4 mM CaCl2), detergent (1.8 mM Triton X-100), and precipitant (16% PEG 3350, 4% Tacsimate pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.73	54.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 235.52	α = 90
b = 77.493	β = 112.45
c = 157.966	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	100	CCD	MAR CCD 165 mm			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CAMD BEAMLINE GCPCC	1.38000	CAMD	GCPCC

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	3.5	39.2	98.2	0.135		3.4		32748		-3

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	3.5	3.63	86.8		0.364	1.84	2.6	2833

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 entries 2FNQ, 1U5U	3.51	20.86	30961	1644	98.09	0.27513	0.27264	0.26	0.32191	0.3	RANDOM	2.001

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]
-1.45		-4.14	-0.56		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.532
r_dihedral_angle_4_deg	18.671
r_dihedral_angle_3_deg	18.552
r_dihedral_angle_1_deg	5.509
r_angle_refined_deg	1.234
r_symmetry_vdw_refined	0.349
r_nbtor_refined	0.317
r_nbd_refined	0.253
r_xyhbond_nbd_refined	0.176
r_chiral_restr	0.082
r_symmetry_hbond_refined	0.08
r_metal_ion_refined	0.048
r_bond_refined_d	0.01
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16130
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	88

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing