4HFJ

X-ray Crystal Structure of a Double Bond Reductase from Nicotiana tabacum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3J3H 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.5293100mM KH2PO4/citrate buffer pH 4.5 + 45% PEG 300, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5752.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.57α = 90
b = 148.74β = 115.59
c = 67.73γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2011-01-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.979DiamondI04

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
11.9442.130.05515.54.857956

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3J3H242.134992326861000.184550.182220.22737RANDOM32.739
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]
0.01-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.305
r_dihedral_angle_4_deg18.366
r_dihedral_angle_3_deg15.409
r_dihedral_angle_1_deg6.39
r_scangle_it3.999
r_scbond_it2.625
r_mcangle_it1.689
r_angle_refined_deg1.541
r_mcbond_it0.997
r_chiral_restr0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.305
r_dihedral_angle_4_deg18.366
r_dihedral_angle_3_deg15.409
r_dihedral_angle_1_deg6.39
r_scangle_it3.999
r_scbond_it2.625
r_mcangle_it1.689
r_angle_refined_deg1.541
r_mcbond_it0.997
r_chiral_restr0.115
r_bond_refined_d0.018
r_gen_planes_refined0.009
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5006
Nucleic Acid Atoms
Solvent Atoms301
Heterogen Atoms

Software

Software
Software NamePurpose
GDAdata collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling