5OWP

Crystal structure of glycopeptide "GVTSAfPDT*RPAP" in complex with scFv-SM3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5A2K 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 3350, disodium hydrogen phosphate
Crystal Properties
Matthews coefficientSolvent content
1.9837.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.399α = 90
b = 68.151β = 90
c = 90.358γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 S 6M2016-02-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.97DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)CC (Half)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
11.8590.3699.70.0490.99810.96.419335
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9599.80.3940.6851.96.3

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 REPLACEMENTTHROUGHOUT5A2K1.8590.361872756199.70.195990.194280.25614RANDOM33.899
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]
1.580.64-2.23
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.812
r_dihedral_angle_4_deg19.794
r_dihedral_angle_3_deg15.228
r_dihedral_angle_1_deg7.458
r_long_range_B_refined6.06
r_long_range_B_other6.059
r_scangle_other2.808
r_mcangle_other2.418
r_mcangle_it2.417
r_angle_refined_deg1.854
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.812
r_dihedral_angle_4_deg19.794
r_dihedral_angle_3_deg15.228
r_dihedral_angle_1_deg7.458
r_long_range_B_refined6.06
r_long_range_B_other6.059
r_scangle_other2.808
r_mcangle_other2.418
r_mcangle_it2.417
r_angle_refined_deg1.854
r_scbond_it1.791
r_scbond_other1.79
r_mcbond_it1.507
r_mcbond_other1.502
r_angle_other_deg1.229
r_chiral_restr0.107
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d0.005
r_gen_planes_other0.002
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1777
Nucleic Acid Atoms
Solvent Atoms143
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing