6QPD

Engineered beta-lactoglobulin: variant I56F


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2932.60 M (NH4)2SO4 in 0.1 M Tris-HCl pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.5451.63

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.272α = 90
b = 53.272β = 90
c = 113.051γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDAGILENT ATLAS CCD2015-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEAgilent SuperNova1.5406

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
1213.8198.50.0880.110.0650.9937.42.512897
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)
122.0596.40.4460.6060.4070.5961.72

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 REPLACEMENTTHROUGHOUT1BSY213.8111587130898.080.21360.20740.2687RANDOM28.2
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
r_dihedral_angle_2_deg36.443
r_dihedral_angle_3_deg17.318
r_dihedral_angle_4_deg15.967
r_dihedral_angle_1_deg7.174
r_long_range_B_refined6.258
r_long_range_B_other6.179
r_scangle_other3.758
r_mcangle_it3.03
r_mcangle_other3.028
r_scbond_it2.279
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.443
r_dihedral_angle_3_deg17.318
r_dihedral_angle_4_deg15.967
r_dihedral_angle_1_deg7.174
r_long_range_B_refined6.258
r_long_range_B_other6.179
r_scangle_other3.758
r_mcangle_it3.03
r_mcangle_other3.028
r_scbond_it2.279
r_scbond_other2.279
r_mcbond_it1.897
r_mcbond_other1.896
r_angle_refined_deg1.362
r_angle_other_deg0.772
r_chiral_restr0.068
r_bond_refined_d0.01
r_gen_planes_refined0.006
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 Atoms1242
Nucleic Acid Atoms
Solvent Atoms176
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
PHASERphasing