8AMH

The Crystal structure of wt apo agroavidin


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29325% PEG 3350, 0.1 M MgCl2, 0.1 M Bis-Tris pH 6
Crystal Properties
Matthews coefficientSolvent content
1.9837.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.853α = 90
b = 83.639β = 90
c = 67.781γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2018-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID091.072ESRFID09

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
11.7344.4499.50.0610.9913.85.147014
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.731.7999.11.090.639

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 REPLACEMENTTHROUGHOUTrhizavidin1.7344.4447014254899.370.193740.192350.21836RANDOM28.28
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]
0.02-0.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.242
r_dihedral_angle_4_deg16.338
r_dihedral_angle_3_deg13.592
r_dihedral_angle_1_deg7.039
r_long_range_B_refined6.531
r_long_range_B_other6.531
r_scangle_other5.155
r_mcangle_it3.619
r_mcangle_other3.619
r_scbond_it3.426
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.242
r_dihedral_angle_4_deg16.338
r_dihedral_angle_3_deg13.592
r_dihedral_angle_1_deg7.039
r_long_range_B_refined6.531
r_long_range_B_other6.531
r_scangle_other5.155
r_mcangle_it3.619
r_mcangle_other3.619
r_scbond_it3.426
r_scbond_other3.425
r_mcbond_it2.53
r_mcbond_other2.52
r_angle_refined_deg1.687
r_angle_other_deg1.474
r_chiral_restr0.08
r_bond_refined_d0.011
r_gen_planes_refined0.009
r_bond_other_d0.005
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 Atoms3666
Nucleic Acid Atoms
Solvent Atoms158
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing