X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LSH1LSH, 4EKZ
experimental modelPDB 4EKZ1LSH, 4EKZ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52770.1 M Tris pH 8.25, 0.2 M Li2SO4, 32% v/v PEG 400, 2% Polypropylene glycol P425
Crystal Properties
Matthews coefficientSolvent content
2.7955.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 77.537α = 89.81
b = 105.595β = 76.95
c = 112.269γ = 74.24
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2M2017-05-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE MASSIF-10.966ESRFMASSIF-1

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
12.549.3593.80.060.0860.9988.481.69410827971.063
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)
12.52.6590.71.2021.70.2760.631.722

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 REPLACEMENTTHROUGHOUT1LSH, 4EKZ2.549.35102860541493.810.20710.20450.2571RANDOM72.488
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]
2.510.63-2.06-0.52-1.77-1.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.377
r_dihedral_angle_4_deg20.184
r_dihedral_angle_3_deg20.137
r_dihedral_angle_1_deg7.214
r_angle_refined_deg1.356
r_chiral_restr0.105
r_bond_refined_d0.006
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms20821
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms342

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing