2A5C

Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1IJ8PDB entry 1ij8

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52900.2M ammonium sulphate, 0.1M Na Cacodylate pH6.5, 30% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties
Matthews coefficientSolvent content
2.140.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.584α = 90
b = 79.052β = 90
c = 42.997γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42004-12-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX14.20.9795SRSPX14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.552.7970.1020.10218.28.1880785382239.5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.5995.995.90.710.712.38.3822

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (All)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 REPLACEMENTTHROUGHOUTPDB entry 1ij82.552.728538851540096.920.2250.2250.2210.308RANDOM39.447
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]
2-0.4-1.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.708
r_dihedral_angle_4_deg22.468
r_dihedral_angle_3_deg18.794
r_dihedral_angle_1_deg8.67
r_scangle_it3.326
r_angle_refined_deg2.17
r_scbond_it1.969
r_mcangle_it1.793
r_mcbond_it1.054
r_nbtor_refined0.315
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.708
r_dihedral_angle_4_deg22.468
r_dihedral_angle_3_deg18.794
r_dihedral_angle_1_deg8.67
r_scangle_it3.326
r_angle_refined_deg2.17
r_scbond_it1.969
r_mcangle_it1.793
r_mcbond_it1.054
r_nbtor_refined0.315
r_symmetry_vdw_refined0.253
r_nbd_refined0.225
r_symmetry_hbond_refined0.183
r_xyhbond_nbd_refined0.173
r_chiral_restr0.145
r_bond_refined_d0.017
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1924
Nucleic Acid Atoms
Solvent Atoms26
Heterogen Atoms66

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction