2DIO | pdb_00002dio

Crystal Structure of the Allene Oxide Cyclase 2 with bound inhibitor vernolic acid

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	291	10% PEG3350, 200mM NaCl, 100mM phosphate citrate, pH 4.2, vapor diffusion, hanging drop, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.5	α = 90
b = 99.8	β = 90
c = 105.9	γ = 90

Symmetry
Space Group	P 21 21 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	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2004-12-08	M	SINGLE WAVELENGTH
2	1	x-ray		M

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	CU K-ALPHA	1.54
2

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
1,2	1.7	38	93.5	0.079	15.2	4.2	70876	70876			18.165

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.7	1.8	89.8	89.4	0.345	4.2	4.2	10561

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2BRJ	1.7	38	70876	70876	3583	93.5	0.199	0.199	0.197	0.1978	0.232	0.229	RANDOM	12.916

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]
0.02			-0.34		0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.871
r_dihedral_angle_3_deg	14.275
r_dihedral_angle_4_deg	9.037
r_dihedral_angle_1_deg	6.933
r_scangle_it	4.134
r_scbond_it	2.939
r_angle_refined_deg	1.784
r_mcangle_it	1.693
r_mcbond_it	1.125
r_nbtor_refined	0.31
r_chiral_restr	0.234
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.168
r_xyhbond_nbd_refined	0.144
r_symmetry_hbond_refined	0.144
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4092
Nucleic Acid Atoms
Solvent Atoms	368
Heterogen Atoms	51

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction