5MXB

Crystal structure of yellow lupin LLPR-10.2B protein in complex with melatonin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.32921.4 M sodium citrate pH 6.3
Crystal Properties
Matthew coefficientSolvent content
3.2662.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.469α = 90
b = 74.469β = 90
c = 67.11γ = 120
Symmetry
Space GroupP 65

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2012-07-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.918410BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
11.5137.2399.70.040.04718.484.06933163-330.38
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.699.40.6950.8032.183.998

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 REPLACEMENTFREE R-VALUE2qim1.5137.2332068109599.710.18380.18290.2107RANDOM29.189
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]
-0.81-0.81-0.812.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.85
r_dihedral_angle_3_deg14
r_dihedral_angle_1_deg5.793
r_dihedral_angle_4_deg5.784
r_angle_refined_deg1.933
r_angle_other_deg0.793
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.015
r_gen_planes_other0.004
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.85
r_dihedral_angle_3_deg14
r_dihedral_angle_1_deg5.793
r_dihedral_angle_4_deg5.784
r_angle_refined_deg1.933
r_angle_other_deg0.793
r_chiral_restr0.115
r_bond_refined_d0.019
r_gen_planes_refined0.015
r_gen_planes_other0.004
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1163
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms54

Software

Software
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing