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Crystal structure of mimicry-recognizing 2D10 scFv with peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H0I PDB ENTRY 4H0I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 100 mM MES, pH 6.5, 1.6 M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.47 50.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.33 α = 90 b = 80.33 β = 90 c = 74.98 γ = 120
Symmetry Space Group P 31 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 120 IMAGE PLATE MAR scanner 345 mm plate mirrors 2008-12-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU300 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 69.568 100 0.065 24.1 10.5 19310 19310
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.11 100 0.427 5.5 10.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 PDB ENTRY 4H0I 2 25.5 19310 17376 1899 99.96 0.19725 0.19524 0.195 0.21525 0.2162 RANDOM 30.55
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] 0.33 0.17 0.33 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.483 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 16.459 r_dihedral_angle_1_deg 4.998 r_scangle_it 4.546 r_scbond_it 3.159 r_mcangle_it 2.538 r_angle_refined_deg 1.865 r_mcbond_it 1.575 r_chiral_restr 0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.483 r_dihedral_angle_4_deg 21.046 r_dihedral_angle_3_deg 16.459 r_dihedral_angle_1_deg 4.998 r_scangle_it 4.546 r_scbond_it 3.159 r_mcangle_it 2.538 r_angle_refined_deg 1.865 r_mcbond_it 1.575 r_chiral_restr 0.168 r_bond_refined_d 0.028 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1914 Nucleic Acid Atoms Solvent Atoms 204 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOLREP phasing CNS refinement MOSFLM data reduction SCALA data scaling MAR345dtb data collection