☰ Navigation Tabs
Crystal structure of murine 4-1BB N128A mutant from HEK293T cells in P43 space group
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 295 0.1 M sodium acetate pH 4.5, 30% w/V PEG 8000, 0.2M lithium sulfate
Crystal Properties Matthews coefficient Solvent content 2.92 57.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.639 α = 90 b = 66.639 β = 90 c = 82.184 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.97 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.18 50 99.4 0.07 0.078 0.033 6.1 5.4 18619
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.18 2.22 97.9 0.493 0.554 0.247 0.821 4.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 5WJF 2.3 47.12 15201 800 99.95 0.1988 0.1972 0.2022 0.2279 0.2184 RANDOM 51.935
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 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.076 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_4_deg 11.953 r_dihedral_angle_1_deg 5.837 r_angle_refined_deg 1.1 r_angle_other_deg 0.82 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.076 r_dihedral_angle_3_deg 12.033 r_dihedral_angle_4_deg 11.953 r_dihedral_angle_1_deg 5.837 r_angle_refined_deg 1.1 r_angle_other_deg 0.82 r_chiral_restr 0.061 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1577 Nucleic Acid Atoms Solvent Atoms 115 Heterogen Atoms 101
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling PDB_EXTRACT data extraction HKL-2000 data reduction REFMAC phasing