2G5W

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)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q45 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293PROTEIN 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 coefficientSolvent content
2.4950.68

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.702α = 90
b = 86.608β = 90
c = 123.583γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDPAIR OF BIMORPH, RHODIUM COATED KIRKPATRICK-BAEZ MIRRORS2005-08-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-D0.98244APS23-ID-D

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.5850820.1579.5496.122750
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.582.67500.3663.4233.91365

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Q452.57648.83422704112581.8840.2050.205120.20210.2643RANDOM39.822
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]
-3.003-4.1357.138
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.206
r_dihedral_angle_3_deg14.839
r_dihedral_angle_4_deg14.239
r_dihedral_angle_1_deg5.059
r_scangle_it2.301
r_scbond_it1.503
r_mcangle_it1.071
r_angle_refined_deg0.977
r_mcbond_it0.552
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.206
r_dihedral_angle_3_deg14.839
r_dihedral_angle_4_deg14.239
r_dihedral_angle_1_deg5.059
r_scangle_it2.301
r_scbond_it1.503
r_mcangle_it1.071
r_angle_refined_deg0.977
r_mcbond_it0.552
r_nbtor_refined0.302
r_nbd_refined0.183
r_symmetry_vdw_refined0.164
r_symmetry_hbond_refined0.125
r_xyhbond_nbd_refined0.117
r_chiral_restr0.063
r_bond_refined_d0.006
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5623
Nucleic Acid Atoms
Solvent Atoms108
Heterogen Atoms110

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing