5YSL

Crystal structure of antibody 1H1 Fab


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.8291.150.2 M potassium sulfate, 20% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.4148.97

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.183α = 85.68
b = 81.091β = 82.85
c = 98.472γ = 71.45
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152016-05-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U10.97915SSRFBL17U1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.55098.313.3262.964042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.52.59

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 REPLACEMENTTHROUGHOUT1SY62.55060791325197.240.215520.212390.27337RANDOM47.266
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]
2.930.150.66-1.32-0.7-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.829
r_dihedral_angle_4_deg23.579
r_dihedral_angle_3_deg19.735
r_long_range_B_other8.402
r_long_range_B_refined8.401
r_dihedral_angle_1_deg8.271
r_scangle_other5.984
r_mcangle_it5.358
r_mcangle_other5.358
r_scbond_it3.911
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.829
r_dihedral_angle_4_deg23.579
r_dihedral_angle_3_deg19.735
r_long_range_B_other8.402
r_long_range_B_refined8.401
r_dihedral_angle_1_deg8.271
r_scangle_other5.984
r_mcangle_it5.358
r_mcangle_other5.358
r_scbond_it3.911
r_scbond_other3.91
r_mcbond_it3.595
r_mcbond_other3.593
r_angle_refined_deg1.787
r_angle_other_deg1.049
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d0.002
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 Atoms12923
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing