1VYO

Crystal structure of avidin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1AVDPDB ENTRY 1AVD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.6295Equal volumes (1 ul) of protein (0.5 mg/ml) in 50 mM Na acetate (pH 4) + 20 mM NaCl and well solution of 0.1 M MES (pH 6.6) + 24% PEG 8000 + 0.2 M Mg acetate
Crystal Properties
Matthews coefficientSolvent content
2.1542.82

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.949α = 90
b = 78.772β = 90
c = 43.01γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X13EMBL/DESY, HAMBURGX13

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
11.4820990.07310441811
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)
11.481.58990.4734

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1AVD1.4819.13972020911000.1670.1650.19RANDOM7.58
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]
1.13-0.35-0.77
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.972
r_scangle_it3.246
r_scbond_it2.013
r_angle_refined_deg1.483
r_mcangle_it1.226
r_angle_other_deg0.849
r_mcbond_it0.7
r_symmetry_vdw_other0.303
r_nbd_other0.257
r_symmetry_vdw_refined0.247
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.972
r_scangle_it3.246
r_scbond_it2.013
r_angle_refined_deg1.483
r_mcangle_it1.226
r_angle_other_deg0.849
r_mcbond_it0.7
r_symmetry_vdw_other0.303
r_nbd_other0.257
r_symmetry_vdw_refined0.247
r_nbd_refined0.192
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.141
r_chiral_restr0.097
r_nbtor_other0.088
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
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 Atoms1905
Nucleic Acid Atoms
Solvent Atoms149
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
AMoREphasing