1DZB

Crystal structure of phage library-derived single-chain Fv fragment 1F9 in complex with turkey egg-white lysozyme


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15A SOLUTION OF SCFV FRAGMENT 1F9/TEL COMPLEX IN A 1:1 RATION IN 5 MM TRIS/HCL PH 7.5, 0.1 M NACL WAS MIXED WITH 10% PEG4000, 0.1 M AMMONIUMACETAT AND 0.05 M SODIUMACETATE BUFFER PH 5.0 AND EQUILIBRATED AGAINST 30% PEG4000
Crystal Properties
Matthews coefficientSolvent content
2.7535.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 38.71α = 90
b = 112.44β = 97.67
c = 80γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1998-07-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X31EMBL/DESY, HAMBURGX31

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
122587.90.13912.17.44024027.683
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)
122.0775.50.1963.77

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1JHL22040205201187.90.2250.306RANDOM32.3
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]
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor28.1
p_staggered_tor21.3
p_plane_restr10.6
p_planar_tor10.6
p_scangle_it4.209
p_mcangle_it4.025
p_scbond_it2.923
p_mcbond_it2.719
p_multtor_nbd0.264
p_singtor_nbd0.194
RMS Deviations
KeyRefinement Restraint Deviation
p_transverse_tor28.1
p_staggered_tor21.3
p_plane_restr10.6
p_planar_tor10.6
p_scangle_it4.209
p_mcangle_it4.025
p_scbond_it2.923
p_mcbond_it2.719
p_multtor_nbd0.264
p_singtor_nbd0.194
p_chiral_restr0.166
p_xhyhbond_nbd0.165
p_planar_d0.083
p_angle_d0.045
p_bond_d0.015
p_angle_deg
p_hb_or_metal_coord
p_xyhbond_nbd
p_orthonormal_tor
p_special_tor
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5442
Nucleic Acid Atoms
Solvent Atoms260
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing