2Y32

Crystal structure of bradavidin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP0.7 MICROLITER OF WELL SOLUTION CONTAINING 25% PEG 4000, 0.17 M AMMONIUM ACETATE, AND 0.08 M SODIUM ACETATE, PH 4.6 WERE MIXED WITH 0.8 MICROLITER OF PROTEIN SOLUTION CONTAINING 0.4 MG PER ML OF PROTEIN, 50 MM SODIUM ACETATE, PH 4. THE PROTEIN SOLUTION WAS DILUTED WITH SATURATED SOLUTION OF 4-HYDROXYAZOBENZENE-2-CARBOXYLIC ACID IN 1 TO 10 VOLUME RATIO BEFORE CRYSTALLIZATION, WHICH WAS AT RT USING THE VAPOUR DIFFUSION METHOD AND SITTING DROPS.
Crystal Properties
Matthews coefficientSolvent content
2.141

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.712α = 90
b = 84.868β = 90
c = 120.26γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH SX-1652006-06-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONMAX II BEAMLINE I911-2MAX III911-2

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
11.78251000.09189.646670-3
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)
11.781.881000.425.99.6

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 REPLACEMENTTHROUGHOUTAN ENSEMBLE OF THREE HOMOLOGY MODELS OF BRADAVIDIN BASED ON PDB ENTRIES 1AVD, 1MK5, AND 2UYW.1.7828.644430323651000.146390.14440.18243RANDOM18.011
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]
-0.350.180.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.523
r_dihedral_angle_3_deg11.221
r_dihedral_angle_1_deg5.904
r_scangle_it3.159
r_scbond_it2.142
r_angle_refined_deg1.382
r_mcangle_it1.346
r_mcbond_it0.76
r_chiral_restr0.112
r_bond_refined_d0.014
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.523
r_dihedral_angle_3_deg11.221
r_dihedral_angle_1_deg5.904
r_scangle_it3.159
r_scbond_it2.142
r_angle_refined_deg1.382
r_mcangle_it1.346
r_mcbond_it0.76
r_chiral_restr0.112
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_4_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4034
Nucleic Acid Atoms
Solvent Atoms680
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing