4NH4

Structure of the binary complex of a zingiber officinale double bond reductase in complex with NADP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.529821% PEG 1450, 100mM PCB, 3mM NaN3, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3146.86

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.66α = 90
b = 78.406β = 90
c = 155.706γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCDPT COATED SI MIRRORS2013-10-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.87260ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.178.03799.30.09112.84.54386843868-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.2199.90.7450.7450.8430.3890.94.66310

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4MKR2.155.314378743787225099.070.19640.19640.1930.2598RANDOM39.061
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]
0.010.45-0.46
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.737
r_dihedral_angle_3_deg14.688
r_dihedral_angle_4_deg12.697
r_dihedral_angle_1_deg7.032
r_mcangle_it3.152
r_mcbond_it2.13
r_mcbond_other2.13
r_angle_refined_deg1.815
r_angle_other_deg0.848
r_chiral_restr0.099
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.737
r_dihedral_angle_3_deg14.688
r_dihedral_angle_4_deg12.697
r_dihedral_angle_1_deg7.032
r_mcangle_it3.152
r_mcbond_it2.13
r_mcbond_other2.13
r_angle_refined_deg1.815
r_angle_other_deg0.848
r_chiral_restr0.099
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5391
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms96

Software

Software
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
XDSdata reduction