2G5W | pdb_00002g5w

X-ray crystal structure of Arabidopsis thaliana 12-oxophytodienoate reductase isoform 3 (AtOPR3) in complex with 8-iso prostaglandin A1 and its cofactor, flavin mononucleotide.

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q45

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	PROTEIN SOLUTION (10 MG/ML PROTEIN, 0.10 M SODIUM CHLORIDE, 0.0003 M TECP, 0.010 M MES, pH 6.0) MIXED IN A 1:1 RATIO WITH THE WELL SOLUTION (8.75-10.0% MEPEG 5000, 0.275-0.350 M GLYCINE, 0.10 M TRIETHANOLAMINE pH 8.0), vapor diffusion, hanging drop, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.68

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.702	α = 90
b = 86.608	β = 90
c = 123.583	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	CCD	MARMOSAIC 300 mm CCD	PAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS	2005-08-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	0.98244	APS	23-ID-D

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	2.58	50	82	0.157	9.549	6.1		22750

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	2.58	2.67	50		0.366	3.423	3.9	1365

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	1Q45	2.576	48.834	22704	1125	81.884	0.205	0.20512	0.2021	0.2	0.2643	0.27	RANDOM	39.822

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]
-3.003			-4.135		7.138

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.206
r_dihedral_angle_3_deg	14.839
r_dihedral_angle_4_deg	14.239
r_dihedral_angle_1_deg	5.059
r_scangle_it	2.301
r_scbond_it	1.503
r_mcangle_it	1.071
r_angle_refined_deg	0.977
r_mcbond_it	0.552
r_nbtor_refined	0.302

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.206
r_dihedral_angle_3_deg	14.839
r_dihedral_angle_4_deg	14.239
r_dihedral_angle_1_deg	5.059
r_scangle_it	2.301
r_scbond_it	1.503
r_mcangle_it	1.071
r_angle_refined_deg	0.977
r_mcbond_it	0.552
r_nbtor_refined	0.302
r_nbd_refined	0.183
r_symmetry_vdw_refined	0.164
r_symmetry_hbond_refined	0.125
r_xyhbond_nbd_refined	0.117
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5623
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	110

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOLREP	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.