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Fab fragment of antibody against fullerene C60
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MFB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 25 % w/v PEG 3350, 0.2 M (NH4)2SO4, 0.1 M Bis-Tris, pH 6.5
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.33 α = 90 b = 138.18 β = 91.85 c = 83.53 γ = 90
Symmetry Space Group P 1 21 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 SX-165mm 2014-02-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON KURCHATOV SNC BEAMLINE K4.4 0.98 KURCHATOV SNC K4.4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.91 28.83 99.5 0.084 0.999 17.5 5 69665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.91 2.02 97.3 0.569 0.83 4.8
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 FREE R-VALUE 1MFB 1.92 28.83 66144 3520 99.43 0.19051 0.18819 0.1909 0.23354 0.2365 RANDOM 30.3
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] 0.9 -0.23 0.4 -1.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.691 r_dihedral_angle_4_deg 22.392 r_dihedral_angle_3_deg 14.547 r_dihedral_angle_1_deg 7.237 r_long_range_B_refined 6.271 r_mcangle_it 3.786 r_scbond_it 3.39 r_mcbond_it 2.705 r_angle_refined_deg 1.911 r_chiral_restr 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.691 r_dihedral_angle_4_deg 22.392 r_dihedral_angle_3_deg 14.547 r_dihedral_angle_1_deg 7.237 r_long_range_B_refined 6.271 r_mcangle_it 3.786 r_scbond_it 3.39 r_mcbond_it 2.705 r_angle_refined_deg 1.911 r_chiral_restr 0.132 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 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_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6491 Nucleic Acid Atoms Solvent Atoms 456 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling BALBES phasing