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Structure antibody E6 in complex with methylated peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6LDV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293.15 0.1 M potassium chloride
24% PEG3350
Crystal Properties Matthews coefficient Solvent content 1.96 37.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.329 α = 90 b = 82.329 β = 90 c = 120.269 γ = 90
Symmetry Space Group P 41 21 2
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 EIGER X 4M 2019-03-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-1A 1.000 Photon Factory BL-1A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.8 67.94 99.9 0.092 0.019 0.999 23.3 23.2 39032
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.1 0.468 0.131 0.875 5.6 13.5
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 6LDV 1.8 67.94 37400 1562 99.83 0.1713 0.1694 0.1792 0.2173 0.2231 RANDOM 21.935
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] 0.13 0.13 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.41 r_dihedral_angle_4_deg 17.676 r_dihedral_angle_3_deg 12.907 r_dihedral_angle_1_deg 7.445 r_angle_refined_deg 1.857 r_angle_other_deg 1.483 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.41 r_dihedral_angle_4_deg 17.676 r_dihedral_angle_3_deg 12.907 r_dihedral_angle_1_deg 7.445 r_angle_refined_deg 1.857 r_angle_other_deg 1.483 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3223 Nucleic Acid Atoms Solvent Atoms 331 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing