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Crystal structure of rabbit antibody with phosphorylated peptide bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4HBC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 293.15 0.2 M Lithium chloride,
20 % w/v Polyethylene glycol 3350
Crystal Properties Matthews coefficient Solvent content 2.12 42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.52 α = 71.31 b = 43.56 β = 84.39 c = 63.52 γ = 87.57
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 ADSC QUANTUM 270 2016-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.0000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.4 41.3 88.8 0.092 0.977 5.7 1.9 77744
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.47 0.368 0.65 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.4 29.86 75415 2329 88.78 0.16321 0.16202 0.1712 0.1993 0.204 RANDOM 11.213
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] -0.87 0.01 -0.1 -0.42 -0.44 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.028 r_dihedral_angle_1_deg 7.775 r_dihedral_angle_2_deg 6.965 r_rigid_bond_restr 3.442 r_long_range_B_refined 2.071 r_long_range_B_other 1.882 r_angle_refined_deg 1.609 r_scangle_other 1.315 r_mcangle_it 1.218 r_mcangle_other 1.218
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.028 r_dihedral_angle_1_deg 7.775 r_dihedral_angle_2_deg 6.965 r_rigid_bond_restr 3.442 r_long_range_B_refined 2.071 r_long_range_B_other 1.882 r_angle_refined_deg 1.609 r_scangle_other 1.315 r_mcangle_it 1.218 r_mcangle_other 1.218 r_scbond_it 0.931 r_scbond_other 0.931 r_mcbond_it 0.915 r_mcbond_other 0.897 r_angle_other_deg 0.563 r_chiral_restr 0.084 r_gen_planes_refined 0.01 r_bond_refined_d 0.009 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3557 Nucleic Acid Atoms Solvent Atoms 457 Heterogen Atoms 2
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing