5MYQ

Crystal structure of avidin in complex with ferrocene homobiotin derivative


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP292.150.2 M ammonium iodide, 22 % w/v PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.2545.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 43.933α = 90
b = 82.081β = 106.29
c = 74.601γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-09-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.91840BESSY14.2

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
11.8971.697.10.0529.361.9242387

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 REPLACEMENTTHROUGHOUT1VYO1.8971.638729122998.650.187110.185670.23201RANDOM34.481
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]
1.25-0.65-2.081.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.508
r_dihedral_angle_4_deg21.482
r_dihedral_angle_3_deg15.088
r_dihedral_angle_1_deg7.412
r_long_range_B_refined6.609
r_long_range_B_other6.609
r_angle_refined_deg2.185
r_scangle_other2.139
r_mcangle_other2.134
r_mcangle_it2.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.508
r_dihedral_angle_4_deg21.482
r_dihedral_angle_3_deg15.088
r_dihedral_angle_1_deg7.412
r_long_range_B_refined6.609
r_long_range_B_other6.609
r_angle_refined_deg2.185
r_scangle_other2.139
r_mcangle_other2.134
r_mcangle_it2.133
r_scbond_it1.559
r_scbond_other1.558
r_mcbond_it1.264
r_mcbond_other1.261
r_angle_other_deg1.115
r_chiral_restr0.111
r_bond_refined_d0.019
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms3828
Nucleic Acid Atoms
Solvent Atoms337
Heterogen Atoms181

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing