3TPK

Crystal structure of the oligomer-specific KW1 antibody fragment


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LN9PDB entry 3LN9

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.9288200 mM Magnesium Formate, 20%(w/v)PEG 3350, Additive: Benzamidine Hydrochloride 1M , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Crystal Properties
Matthews coefficientSolvent content
1.8734.16

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 30.921α = 90
b = 38.659β = 90
c = 94.412γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-05-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

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
11.213089.30.03119.863.235385316062-316.062
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)
11.211.2446.80.3831.85

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 3LN91.325.87316062780413911000.1430.1430.14120.1761RANDOM15.3404
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]
0.23-0.03-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.513
r_dihedral_angle_4_deg14.893
r_sphericity_free13.191
r_dihedral_angle_3_deg12.221
r_sphericity_bonded8.294
r_dihedral_angle_1_deg6.522
r_scangle_it6.44
r_scbond_it4.718
r_mcangle_it3.944
r_rigid_bond_restr2.794
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.513
r_dihedral_angle_4_deg14.893
r_sphericity_free13.191
r_dihedral_angle_3_deg12.221
r_sphericity_bonded8.294
r_dihedral_angle_1_deg6.522
r_scangle_it6.44
r_scbond_it4.718
r_mcangle_it3.944
r_rigid_bond_restr2.794
r_mcbond_it2.73
r_angle_refined_deg2.046
r_chiral_restr0.147
r_bond_refined_d0.026
r_gen_planes_refined0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms934
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms13

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction