5HTD

Recombinant bovine beta-lactoglobulin variant L1A/I2S with endogenous ligand (sBlgB#1)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BSY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2981.34 M sodium citrate in 0.1 M Tris pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.5151.09

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.486α = 90
b = 53.486β = 90
c = 111.039γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDAGILENT ATLAS CCD2013-12-02MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEAgilent SuperNova1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.513.7598.90.0728.42.86699
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.6298.80.3481.82.3

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 REPLACEMENTTHROUGHOUT1BSY2.513.755367129398.290.214180.200760.27232RANDOM37.435
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]
0.040.020.04-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg20.246
r_dihedral_angle_3_deg16.483
r_dihedral_angle_1_deg6.023
r_long_range_B_refined5.002
r_long_range_B_other4.964
r_mcangle_it3.213
r_mcangle_other3.211
r_scangle_other2.662
r_mcbond_it1.807
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.263
r_dihedral_angle_4_deg20.246
r_dihedral_angle_3_deg16.483
r_dihedral_angle_1_deg6.023
r_long_range_B_refined5.002
r_long_range_B_other4.964
r_mcangle_it3.213
r_mcangle_other3.211
r_scangle_other2.662
r_mcbond_it1.807
r_mcbond_other1.806
r_scbond_it1.51
r_scbond_other1.509
r_angle_refined_deg1.116
r_angle_other_deg0.715
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1239
Nucleic Acid Atoms
Solvent Atoms35
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing