7BH0

Mutant L39Y of recombinant beta-lactoglobulin in complex with endogenous ligand


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.12932.2 M ammonium sulfate in 0.5 M Tris-HCl pH 7.1
Crystal Properties
Matthews coefficientSolvent content
2.4650.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.27α = 90
b = 53.27β = 90
c = 109.89γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAGILENT ATLAS CCD2015-03-15MSINGLE 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)Rrim I (All)Rpim 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
12.113.7499.40.0580.070.0380.9987.72.711001
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.1698.50.2230.30.1990.88422.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 REPLACEMENTTHROUGHOUT1BSY2.113.66110981106699.1330.2080.2080.20080.2754RANDOM36.239
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]
0.0750.0370.075-0.243
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.049
r_dihedral_angle_3_deg16.547
r_lrange_other11.821
r_lrange_it11.807
r_scangle_it11.433
r_scangle_other11.427
r_scbond_it10.248
r_scbond_other10.24
r_mcangle_it8.631
r_mcangle_other8.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.049
r_dihedral_angle_3_deg16.547
r_lrange_other11.821
r_lrange_it11.807
r_scangle_it11.433
r_scangle_other11.427
r_scbond_it10.248
r_scbond_other10.24
r_mcangle_it8.631
r_mcangle_other8.625
r_dihedral_angle_4_deg7.997
r_mcbond_it7.607
r_mcbond_other7.603
r_dihedral_angle_1_deg7.219
r_angle_refined_deg1.686
r_angle_other_deg1.239
r_nbd_other0.294
r_nbd_refined0.21
r_symmetry_xyhbond_nbd_refined0.198
r_symmetry_nbd_other0.191
r_xyhbond_nbd_refined0.188
r_symmetry_nbd_refined0.174
r_nbtor_refined0.157
r_symmetry_nbtor_other0.08
r_chiral_restr0.07
r_bond_refined_d0.01
r_gen_planes_refined0.008
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1161
Nucleic Acid Atoms
Solvent Atoms86
Heterogen Atoms15

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction