4HFM

X-ray Crystal Structure of a NADP(H)-bound 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
2.5351.44

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.2α = 90
b = 149.84β = 115.53
c = 66.61γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2011-02-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.979DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.960.115.859835

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3J3H1.957.83256799303597.680.174560.172910.20553RANDOM27.215
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]
-0.04-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.646
r_dihedral_angle_4_deg18.22
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg6.273
r_scangle_it4.059
r_scbond_it2.557
r_mcangle_it1.64
r_angle_refined_deg1.612
r_mcbond_it0.92
r_chiral_restr0.119
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.646
r_dihedral_angle_4_deg18.22
r_dihedral_angle_3_deg14.761
r_dihedral_angle_1_deg6.273
r_scangle_it4.059
r_scbond_it2.557
r_mcangle_it1.64
r_angle_refined_deg1.612
r_mcbond_it0.92
r_chiral_restr0.119
r_bond_refined_d0.016
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5027
Nucleic Acid Atoms
Solvent Atoms307
Heterogen Atoms96

Software

Software
Software NamePurpose
GDAdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling