5MXW

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin and trans-zeatin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QIM 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32921.4 M sodium citrate pH 6.3
Crystal Properties
Matthews coefficientSolvent content
3.2462.05

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.4α = 90
b = 74.4β = 90
c = 67.31γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-12-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-21.0000000MAX III911-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)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
11.5746.5999.70.0370.0410.99922.24.98429524-331.574
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.6698.40.7440.8340.7892.014.892

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 REPLACEMENTTHROUGHOUT2qim1.5746.5928468105799.680.18580.1850.2059RANDOM32.201
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]
-0.91-0.91-0.912.96
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.583
r_dihedral_angle_3_deg15.508
r_dihedral_angle_1_deg7.039
r_angle_refined_deg1.866
r_angle_other_deg0.791
r_dihedral_angle_4_deg0.424
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.583
r_dihedral_angle_3_deg15.508
r_dihedral_angle_1_deg7.039
r_angle_refined_deg1.866
r_angle_other_deg0.791
r_dihedral_angle_4_deg0.424
r_chiral_restr0.12
r_bond_refined_d0.019
r_gen_planes_refined0.014
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1162
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing