7BBI

Joint X-ray/neutron room temperature structure of H/D-exchanged PLL lectin


X-RAY DIFFRACTION - NEUTRON DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5C9O 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium acetate, pD 4.2, 8 % (w/v) PEG 4000 dissolved in D2O
Crystal Properties
Matthews coefficientSolvent content
3.0860.12

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.68α = 90
b = 89.34β = 90
c = 159.38γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 315r2018-10-24MSINGLE WAVELENGTH
21neutron293IMAGE PLATELADI III2018-09-03LLAUE
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.980ESRFBM30A
2NUCLEAR REACTORILL BEAMLINE LADI III3.1-4.1ILLLADI III

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (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
11.74698.60.064112.43.55657720.07
22.23982.90.182.82.82185520.07
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.72.020.780.63
22.22.320.46

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENT1.739.841.3556568282898.630.13570.13460.156131.76
NEUTRON DIFFRACTIONMOLECULAR REPLACEMENT2.238.9721821109281.510.21620.2150.239631.76
X-RAY+NEUTRON
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.608
f_angle_d1.3115
f_chiral_restr0.0861
f_bond_d0.0102
f_plane_restr0.0065
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2750
Nucleic Acid Atoms
Solvent Atoms340
Heterogen Atoms

Software

Software
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SCALAdata scaling
PHENIXphasing