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X-ray structure of the MK5890 Fab - CD27 antibody-antigen complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2XTJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 0.1M Tris Cl pH 8.5, 40% v/v PEG400, 8.0mM CdCl2
Crystal Properties Matthews coefficient Solvent content 3.6 65.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.246 α = 90 b = 126.105 β = 90 c = 131.602 γ = 90
Symmetry Space Group C 2 2 21
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 PILATUS 6M 2017-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 1. APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.926 52.4 91.5 0.062 0.067 0.026 0.999 15.4 6.6 45883 46.8
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 1.927 2.105 62.6 0.952 1.038 0.408 0.718 6
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 2XTJ 1.926 22 45831 2190 63.8 0.2101 0.2093 0.2129 0.2254 0.2344 RANDOM 59.95
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] 6.0659 -3.3694 -2.6966
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.05 t_omega_torsion 3.74 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.05 t_omega_torsion 3.74 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3980 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 309
Software Software Software Name Purpose XDS data reduction Aimless data scaling MOLREP phasing BUSTER refinement PDB_EXTRACT data extraction