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Crystal Structure Analysis of the Epitope of an Anti-MICA Antibody
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F3D 1F3D, 4M1G, 1HYR, 1NZ8 experimental model PDB 4M1G 1F3D, 4M1G, 1HYR, 1NZ8 experimental model PDB 1HYR 1F3D, 4M1G, 1HYR, 1NZ8 experimental model PDB 1NZ8 1F3D, 4M1G, 1HYR, 1NZ8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 0.1 M sodium acetate, pH 4.6, 25% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.28 46.17
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.69 α = 90 b = 50.177 β = 90.85 c = 88.633 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 RAYONIX MX300-HS 2015-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.00 APS 22-ID
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 1.3 35 99.6 0.059 0.07 0.037 8.5 3.5 126363
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 1.3 1.32 96.4 0.56 0.68 0.38 0.793 2.9
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 1F3D, 4M1G, 1HYR, 1NZ8 1.3 35 120157 6152 99.56 0.1892 0.1884 0.1972 0.2054 0.2146 RANDOM 20.983
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] 0.05 -0.79 -1.75 1.72
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.965 r_dihedral_angle_4_deg 12.958 r_dihedral_angle_3_deg 11.366 r_dihedral_angle_1_deg 6.296 r_angle_refined_deg 1.302 r_angle_other_deg 0.863 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.965 r_dihedral_angle_4_deg 12.958 r_dihedral_angle_3_deg 11.366 r_dihedral_angle_1_deg 6.296 r_angle_refined_deg 1.302 r_angle_other_deg 0.863 r_chiral_restr 0.076 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3880 Nucleic Acid Atoms Solvent Atoms 625 Heterogen Atoms
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing