5A2L

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


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystal Properties
Matthews coefficientSolvent content
1.9436.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.08α = 90
b = 35.19β = 103.01
c = 66.29γ = 90
Symmetry
Space GroupP 1 21 1

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
11.7964.5999.60.117.63.6199051.98
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)
11.791.8899.90.62.43.7

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 1SM31.7964.591930857599.420.1850.184420.20447RANDOM27.314
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]
0.422.33-1.660.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.849
r_dihedral_angle_4_deg19.595
r_dihedral_angle_3_deg14.683
r_dihedral_angle_1_deg6.715
r_mcangle_it3.199
r_scbond_it2.286
r_mcbond_it1.92
r_mcbond_other1.918
r_angle_refined_deg1.528
r_angle_other_deg0.767
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.849
r_dihedral_angle_4_deg19.595
r_dihedral_angle_3_deg14.683
r_dihedral_angle_1_deg6.715
r_mcangle_it3.199
r_scbond_it2.286
r_mcbond_it1.92
r_mcbond_other1.918
r_angle_refined_deg1.528
r_angle_other_deg0.767
r_chiral_restr0.079
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms1759
Nucleic Acid Atoms
Solvent Atoms113
Heterogen Atoms30

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALEPACKdata scaling
MOLREPphasing