6K0Y

Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82930.2M NaCl , 0.1M Tris pH 8, 14% PEG 4K
Crystal Properties
Matthews coefficientSolvent content
2.3547.78

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 39.952α = 90
b = 102.59β = 90
c = 137.723γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 R CdTe 300KQ315r2019-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97918SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
11.741.998.20.1660.0530.99430.21062244
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.71.7380.21.0610.4210.7964.77

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 REPLACEMENTTHROUGHOUT5GGS1.741.959148309598.20.173170.171060.21447RANDOM16.745
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]
-1.481.140.34
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.137
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg12.041
r_dihedral_angle_1_deg7.379
r_long_range_B_refined2.796
r_long_range_B_other2.568
r_mcangle_it1.536
r_mcangle_other1.536
r_scangle_other1.455
r_angle_refined_deg1.246
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.137
r_dihedral_angle_4_deg16.494
r_dihedral_angle_3_deg12.041
r_dihedral_angle_1_deg7.379
r_long_range_B_refined2.796
r_long_range_B_other2.568
r_mcangle_it1.536
r_mcangle_other1.536
r_scangle_other1.455
r_angle_refined_deg1.246
r_angle_other_deg1.194
r_scbond_it1.098
r_scbond_other1.097
r_mcbond_it1.046
r_mcbond_other1.045
r_rigid_bond_restr0.869
r_chiral_restr0.046
r_bond_refined_d0.004
r_gen_planes_refined0.004
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_scangle_it
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4176
Nucleic Acid Atoms
Solvent Atoms492
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing