☰ Navigation Tabs
Crystal structure of mouse PD-L1 nanobody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OL0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 PEG 400, ammonium sulfate, hepes
Crystal Properties Matthews coefficient Solvent content 1.76 30.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.191 α = 90 b = 29.679 β = 90 c = 35.268 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2015-03-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.441 18.23 99.31 23.4 6.9 30989
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1OL0 1.441 18.23 1.11 30989 689 99.31 0.1695 0.1686 0.1685 0.1934 0.1959 Random
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.018 f_angle_d 1.067 f_chiral_restr 0.076 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 885 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 10
Software Software Software Name Purpose PHENIX refinement CBASS data collection HKL-2000 data reduction PHASER phasing HKL-2000 data scaling