5NUM

Engineered beta-lactoglobulin: variant F105L-L39A in complex with chlorpromazine (LG-LA-CLP)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82932.60 M (NH4)2SO4 in 0.1 M Tris-HCl, pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.4950.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.328α = 90
b = 53.328β = 90
c = 110.003γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray130CCDAGILENT ATLAS CCD2016-01-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOXFORD DIFFRACTION NOVA1.54

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
12.31599.30.07482.88447
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)
12.32.3999.50.5761.62.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1bsy2.314.827420100398.880.227930.219460.28908RANDOM43.297
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]
0.010.010.01-0.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.779
r_dihedral_angle_3_deg18.198
r_dihedral_angle_4_deg13.612
r_long_range_B_refined7.635
r_long_range_B_other7.623
r_dihedral_angle_1_deg6.145
r_scangle_other4.978
r_mcangle_it4.351
r_mcangle_other4.349
r_scbond_it3.026
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.779
r_dihedral_angle_3_deg18.198
r_dihedral_angle_4_deg13.612
r_long_range_B_refined7.635
r_long_range_B_other7.623
r_dihedral_angle_1_deg6.145
r_scangle_other4.978
r_mcangle_it4.351
r_mcangle_other4.349
r_scbond_it3.026
r_scbond_other2.994
r_mcbond_it2.668
r_mcbond_other2.668
r_angle_refined_deg1.419
r_angle_other_deg0.764
r_chiral_restr0.08
r_bond_refined_d0.01
r_gen_planes_refined0.005
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 Atoms40
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing