5K06

Recombinant bovine beta-lactoglobulin with uncleaved N-terminal methionine (rBlgB)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2933.0 M (NH4)2SO4 solution in 0.2 M Tris-HCl buffer, pH from 7.8 to 8.8
Crystal Properties
Matthews coefficientSolvent content
2.6453.43

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 106.651α = 90
b = 106.651β = 90
c = 59.312γ = 120
Symmetry
Space GroupP 64 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mm2013-05-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-31.00MAX III911-3

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
12.59.9899.60.07364.719.77101
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)
12.52.541000.22816.120.4

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 REPLACEMENTTHROUGHOUT1BEB2.59.986058104397.80.228810.213220.32372RANDOM39.303
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]
-0.01-0.010.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.007
r_dihedral_angle_3_deg18.883
r_dihedral_angle_4_deg8.684
r_dihedral_angle_1_deg7.595
r_long_range_B_refined7.506
r_long_range_B_other7.503
r_scangle_other4.523
r_mcangle_other4.167
r_mcangle_it4.16
r_scbond_other2.776
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.007
r_dihedral_angle_3_deg18.883
r_dihedral_angle_4_deg8.684
r_dihedral_angle_1_deg7.595
r_long_range_B_refined7.506
r_long_range_B_other7.503
r_scangle_other4.523
r_mcangle_other4.167
r_mcangle_it4.16
r_scbond_other2.776
r_scbond_it2.772
r_mcbond_it2.523
r_mcbond_other2.495
r_angle_refined_deg1.676
r_angle_other_deg0.969
r_chiral_restr0.091
r_bond_refined_d0.012
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 Atoms1244
Nucleic Acid Atoms
Solvent Atoms37
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing