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Crystal structure of the mouse PD-1 Mutant and PD-L2 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BP5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 Sitting drop 8.5 291 20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.55 51.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.747 α = 90 b = 84.335 β = 108 c = 52.281 γ = 90
Symmetry Space Group P 1 21 1
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 315 2007-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 0.9792 NSLS X29A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.6 30 99.7 0.054 16 5.3 47813
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.66 99.5 0.405 4.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 THROUGHOUT 3BP5 1.6 23.98 47784 45379 2405 99.59 0.18583 0.18407 0.1833 0.21833 0.2195 RANDOM 25.773
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.193 r_dihedral_angle_4_deg 21.055 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_1_deg 5.979 r_scangle_it 5.179 r_mcangle_it 3.326 r_scbond_it 3.306 r_mcbond_it 2.198 r_angle_refined_deg 1.251 r_nbtor_refined 0.307
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.193 r_dihedral_angle_4_deg 21.055 r_dihedral_angle_3_deg 14.006 r_dihedral_angle_1_deg 5.979 r_scangle_it 5.179 r_mcangle_it 3.326 r_scbond_it 3.306 r_mcbond_it 2.198 r_angle_refined_deg 1.251 r_nbtor_refined 0.307 r_symmetry_vdw_refined 0.207 r_nbd_refined 0.178 r_xyhbond_nbd_refined 0.15 r_symmetry_hbond_refined 0.147 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2347 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 24
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction CBASS data collection HKL-2000 data reduction PHASES phasing