4Y0R

Bovine beta-lactoglobulin complex with pramocaine crystallized from ammonium sulphate (BLG-PRM2)


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP293protein 20 mg/ml, 2.4 M (NH4)2SO4 in 0.5 M Tris-HCl pH 8.9 and 5 mM pramociane
Crystal Properties
Matthews coefficientSolvent content
2.5251.23

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.735α = 90
b = 53.735β = 90
c = 110.738γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDAGILENT ATLAS CCD2013-04-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SEALED TUBEOTHER1.54

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
12.313.4398.90.05510.42.88567
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)
12.32.4296.60.1622.62.2

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 REPLACEMENTTHROUGHOUT1BSY2.313.437517105098.380.221280.212230.28549RANDOM38.45
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]
-0.01-0.01-0.010.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.925
r_dihedral_angle_3_deg19.375
r_dihedral_angle_4_deg15.557
r_dihedral_angle_1_deg6.641
r_long_range_B_refined5.947
r_long_range_B_other5.945
r_mcangle_it3.954
r_mcangle_other3.952
r_scangle_other3.603
r_mcbond_other2.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg40.925
r_dihedral_angle_3_deg19.375
r_dihedral_angle_4_deg15.557
r_dihedral_angle_1_deg6.641
r_long_range_B_refined5.947
r_long_range_B_other5.945
r_mcangle_it3.954
r_mcangle_other3.952
r_scangle_other3.603
r_mcbond_other2.429
r_mcbond_it2.427
r_scbond_it2.123
r_scbond_other2.121
r_angle_refined_deg1.495
r_angle_other_deg0.788
r_chiral_restr0.073
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 Atoms1226
Nucleic Acid Atoms
Solvent Atoms53
Heterogen Atoms21

Software

Software
Software NamePurpose
REFMACrefinement
CrysalisProdata collection
SCALAdata scaling
PHASERphasing