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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 1A2Y 1A2Y, 4J8R, 1NZ8, 6DDM experimental model PDB 4J8R 1A2Y, 4J8R, 1NZ8, 6DDM experimental model PDB 1NZ8 1A2Y, 4J8R, 1NZ8, 6DDM experimental model PDB 6DDM 1A2Y, 4J8R, 1NZ8, 6DDM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 292 0.01 M ZnSO4, 0.1 M MES, pH 6.5, 16% PEG 550 MME
Crystal Properties Matthews coefficient Solvent content 2.39 48.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.549 α = 90 b = 61.833 β = 90 c = 172.368 γ = 90
Symmetry Space Group P 21 21 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 PILATUS3 6M 2016-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.2 1.00 ALS 5.0.2
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 1.9 35 95 0.085 0.093 0.038 7.7 5.2 42120
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 1.9 1.93 74.6 0.486 0.551 0.254 0.724 4
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 1A2Y, 4J8R, 1NZ8, 6DDM 1.9 35 40023 2050 94.95 0.2103 0.2084 0.214 0.2468 0.2481 RANDOM 33.709
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] -2.11 4.52 -2.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.501 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_3_deg 11.46 r_dihedral_angle_1_deg 5.878 r_angle_refined_deg 1.117 r_angle_other_deg 0.826 r_chiral_restr 0.065 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 35.501 r_dihedral_angle_4_deg 17.905 r_dihedral_angle_3_deg 11.46 r_dihedral_angle_1_deg 5.878 r_angle_refined_deg 1.117 r_angle_other_deg 0.826 r_chiral_restr 0.065 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 3945 Nucleic Acid Atoms Solvent Atoms 260 Heterogen Atoms 54
Software Software Software Name Purpose HKL-2000 data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction PHENIX phasing