5A2K

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.0941.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.418α = 90
b = 68.796β = 90
c = 90.414γ = 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 I04DiamondI04

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
11.7451000.0518.95.4250921.8
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)
11.71.7999.90.5135.5

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 1SM31.790.412430073699.940.176950.175830.21619RANDOM25.937
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]
0.691.46-2.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.297
r_dihedral_angle_4_deg18.376
r_dihedral_angle_3_deg13.786
r_dihedral_angle_1_deg6.982
r_mcangle_it2.418
r_scbond_it1.94
r_angle_refined_deg1.567
r_mcbond_it1.482
r_mcbond_other1.482
r_angle_other_deg0.813
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.297
r_dihedral_angle_4_deg18.376
r_dihedral_angle_3_deg13.786
r_dihedral_angle_1_deg6.982
r_mcangle_it2.418
r_scbond_it1.94
r_angle_refined_deg1.567
r_mcbond_it1.482
r_mcbond_other1.482
r_angle_other_deg0.813
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.001
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 Atoms1757
Nucleic Acid Atoms
Solvent Atoms188
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing