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Crystal structure of 12CA5 Fv-clasp fragment with its antigen peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HIL 1HIL, 5XCQ experimental model PDB 5XCQ 1HIL, 5XCQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 0.1M Na/K phosphate pH6.2, 1.4M (NH4)2SO4
Crystal Properties Matthews coefficient Solvent content 3.18 61.33
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 93.87 α = 90 b = 85.66 β = 125.71 c = 76.54 γ = 90
Symmetry Space Group C 1 2 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 MX300HE 2015-07-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 2.2 42.83 98 0.14 13.6 7.5 24599
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.33 90.2 0.9 3.41 7.3
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 1HIL, 5XCQ 2.2 38.11 23282 1280 98.51 0.21005 0.20817 0.2166 0.244 0.2515 RANDOM 41.11
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] -0.81 0.02 -3.8 2.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.33 r_dihedral_angle_4_deg 17.874 r_dihedral_angle_3_deg 14.319 r_dihedral_angle_1_deg 5.926 r_long_range_B_refined 4.101 r_long_range_B_other 3.653 r_scangle_other 1.863 r_mcangle_it 1.53 r_mcangle_other 1.53 r_angle_refined_deg 1.425
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.33 r_dihedral_angle_4_deg 17.874 r_dihedral_angle_3_deg 14.319 r_dihedral_angle_1_deg 5.926 r_long_range_B_refined 4.101 r_long_range_B_other 3.653 r_scangle_other 1.863 r_mcangle_it 1.53 r_mcangle_other 1.53 r_angle_refined_deg 1.425 r_scbond_it 1.141 r_scbond_other 1.116 r_angle_other_deg 0.923 r_mcbond_it 0.912 r_mcbond_other 0.912 r_chiral_restr 0.083 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2684 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing