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Structure antibody D6 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 0.2 M Calcium chloride
20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.46 50.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.52 α = 85.58 b = 76.21 β = 84.2 c = 79.21 γ = 76.03
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 S 6M 2018-06-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 1.77 40.18 96.9 0.087 0.056 0.993 8.4 3.3 88438
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 1.77 1.87 95.3 0.517 0.335 0.825 2.1 3.3
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 1.77 40.18 84951 3481 96.85 0.1864 0.1851 0.1926 0.2181 0.2234 RANDOM 25.453
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] 1.37 0.76 1.03 -0.81 0.07 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_dihedral_angle_4_deg 12.822 r_dihedral_angle_3_deg 12.508 r_dihedral_angle_1_deg 7.556 r_angle_refined_deg 1.727 r_angle_other_deg 1.444 r_chiral_restr 0.083 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.272 r_dihedral_angle_4_deg 12.822 r_dihedral_angle_3_deg 12.508 r_dihedral_angle_1_deg 7.556 r_angle_refined_deg 1.727 r_angle_other_deg 1.444 r_chiral_restr 0.083 r_bond_refined_d 0.012 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 6468 Nucleic Acid Atoms Solvent Atoms 737 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing