4JJI

Crystal structure of S-nitrosoglutathione reductase from Arabidopsis thalina, complex with NAD+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3UKOPDB entry 3UKO

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52982.1 M ammonium sulfate, 100 mM Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.619α = 90
b = 92.619β = 90
c = 173.171γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 325 mm CCDbent Si-mirror2006-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.9795SSRLBL9-2

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
11.746.899.60.0810.25.7947819478138.2
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)
11.71.761000.343.25.39332

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB entry 3UKO1.838.17602476024401599.620.185230.185230.18320.22348RANDOM32.766
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]
0.030.030.03-0.1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.874
r_dihedral_angle_4_deg19.399
r_dihedral_angle_3_deg15.728
r_dihedral_angle_1_deg6.536
r_angle_refined_deg1.96
r_angle_other_deg0.933
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.874
r_dihedral_angle_4_deg19.399
r_dihedral_angle_3_deg15.728
r_dihedral_angle_1_deg6.536
r_angle_refined_deg1.96
r_angle_other_deg0.933
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5690
Nucleic Acid Atoms
Solvent Atoms465
Heterogen Atoms137

Software

Software
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
CrystalCleardata reduction
CrystalCleardata scaling
REFMACphasing