7BGZ

Mutant L39K 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 DROP8.52933.0 M ammonium sulfate in 0.5 M Tris-HCl pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.5251.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.56α = 90
b = 53.56β = 90
c = 110.88γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDAGILENT ATLAS CCD2014-11-06MSINGLE 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
12.414.2698.10.0570.0670.0340.99812.93.57446
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)
12.42.4997.60.6530.830.5020.7141.42.5

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 REPLACEMENTTHROUGHOUT1BSY2.40113.7537437107597.2790.2040.202970.19380.2663RANDOM50.562
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]
-0.213-0.106-0.2130.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.42
r_dihedral_angle_3_deg18.301
r_dihedral_angle_4_deg8.348
r_dihedral_angle_1_deg7.94
r_lrange_it5.954
r_lrange_other5.95
r_scangle_it4
r_scangle_other3.997
r_mcangle_it3.972
r_mcangle_other3.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.42
r_dihedral_angle_3_deg18.301
r_dihedral_angle_4_deg8.348
r_dihedral_angle_1_deg7.94
r_lrange_it5.954
r_lrange_other5.95
r_scangle_it4
r_scangle_other3.997
r_mcangle_it3.972
r_mcangle_other3.97
r_mcbond_it2.46
r_mcbond_other2.46
r_scbond_it2.456
r_scbond_other2.454
r_angle_refined_deg1.779
r_angle_other_deg1.233
r_nbd_other0.243
r_symmetry_nbd_other0.2
r_nbd_refined0.198
r_nbtor_refined0.159
r_xyhbond_nbd_refined0.138
r_symmetry_nbd_refined0.137
r_symmetry_xyhbond_nbd_refined0.108
r_symmetry_nbtor_other0.086
r_chiral_restr0.075
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1150
Nucleic Acid Atoms
Solvent Atoms49
Heterogen Atoms16

Software

Software
Software NamePurpose
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrysalisProdata reduction