5A2I

Crystal structure of scFv-SM3 in complex with APD-SGalNAc-RP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1SM3PDB ENTRY 1SM3

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.8734.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 33.181α = 90
b = 66.006β = 90
c = 90.29γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I02DiamondI02

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
11.882099.90.0810.46.2168181.8
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)
11.881.9899.90.552.45.6

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 1SM31.8890.291613748498.920.207480.205980.26131RANDOM36.065
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]
-1.935.01-3.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.181
r_dihedral_angle_3_deg17.555
r_dihedral_angle_4_deg17.376
r_dihedral_angle_1_deg7.276
r_mcangle_it3.815
r_scbond_it3.29
r_mcbond_it2.56
r_mcbond_other2.559
r_angle_refined_deg1.829
r_angle_other_deg0.846
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.181
r_dihedral_angle_3_deg17.555
r_dihedral_angle_4_deg17.376
r_dihedral_angle_1_deg7.276
r_mcangle_it3.815
r_scbond_it3.29
r_mcbond_it2.56
r_mcbond_other2.559
r_angle_refined_deg1.829
r_angle_other_deg0.846
r_chiral_restr0.098
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms1748
Nucleic Acid Atoms
Solvent Atoms61
Heterogen Atoms22

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing