6K0Y

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


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8
Temperature 293.0
Details 0.2M NaCl , 0.1M Tris pH 8, 14% PEG 4K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39.95 α = 90
b = 102.59 β = 90
c = 137.72 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS3 R CdTe 300K Q315r 2019-05-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRF BEAMLINE BL17U 0.97918 SSRF BL17U

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.7 41.9 98.2 0.166 -- -- 10.0 -- 62244 -- -- --
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.7 1.73 80.2 1.061 -- 4.7 7.0 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.7 41.9 -- -- -- 59148 3095 98.2 -- 0.17317 0.17106 0.21447 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.7 1.744 -- 199 3633 0.191 0.258 -- 82.27
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.745
Anisotropic B[1][1] -1.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.14
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.34
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.046
r_mcangle_other 1.536
r_bond_refined_d 0.004
r_dihedral_angle_4_deg 16.494
r_gen_planes_other 0.001
r_scbond_other 1.097
r_angle_other_deg 1.194
r_mcbond_other 1.045
r_scbond_it 1.098
r_dihedral_angle_3_deg 12.041
r_long_range_B_other 2.568
r_angle_refined_deg 1.246
r_long_range_B_refined 2.796
r_dihedral_angle_1_deg 7.379
r_bond_other_d 0.001
r_mcbond_it 1.046
r_dihedral_angle_2_deg 31.137
r_mcangle_it 1.536
r_scangle_other 1.455
r_gen_planes_refined 0.004
r_rigid_bond_restr 0.869
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4176
Nucleic Acid Atoms 0
Heterogen Atoms 16
Solvent Atoms 492

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0238
HKL-2000 data reduction
HKL-2000 data scaling
AMoRE phasing