4KRN

Nanobody/VHH domain EgA1


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP629330% PEG3350, 0.2 M ammonium sulfate, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthew coefficientSolvent content
3.0359.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.769α = 90
b = 52.769β = 90
c = 62.724γ = 90
Symmetry
Space GroupP 43

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2008-12-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.980APS23-ID-B

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
11.5531.35799.20.037194.42469424694
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)
11.551.6194.50.2833.52315

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1I3V1.55326.962465123401125399.20.20040.19870.2264RANDOM21.8934
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]
-0.18-0.180.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.72
r_dihedral_angle_4_deg14.875
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg6.059
r_scangle_it2.614
r_scbond_it1.99
r_mcangle_it1.365
r_angle_refined_deg1.111
r_mcbond_it0.822
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.72
r_dihedral_angle_4_deg14.875
r_dihedral_angle_3_deg13.155
r_dihedral_angle_1_deg6.059
r_scangle_it2.614
r_scbond_it1.99
r_mcangle_it1.365
r_angle_refined_deg1.111
r_mcbond_it0.822
r_nbtor_refined0.303
r_nbd_refined0.193
r_symmetry_vdw_refined0.159
r_xyhbond_nbd_refined0.116
r_symmetry_hbond_refined0.09
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms968
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms5

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
JBluIce-EPICSdata collection
HKL-3000data reduction