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Structure of Anticalin N9B in complex with extra-domain B of human oncofetal fibronectin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4GH7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 29 % (w/v) PEG4000, 0.1 M Na-malonate
Crystal Properties Matthews coefficient Solvent content 2.07 40.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.456 α = 90 b = 67.801 β = 90.06 c = 76.806 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 MARMOSAIC 225 mm CCD 2011-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91741 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.6 28.47 99.7 0.057 0.065 0.998 14.85 4.18 70827 -3 25.453
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.7 99.8 0.423 0.485 0.879 3.33 4.172
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 4GH7 1.6 28.47 67277 3545 99.42 0.1707 0.1688 0.174 0.2078 0.212 RANDOM 22.795
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] -10.75 1.05 27.05 -16.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 16.063 r_dihedral_angle_4_deg 14.642 r_dihedral_angle_1_deg 7.508 r_angle_refined_deg 1.918 r_angle_other_deg 1.136 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.343 r_dihedral_angle_3_deg 16.063 r_dihedral_angle_4_deg 14.642 r_dihedral_angle_1_deg 7.508 r_angle_refined_deg 1.918 r_angle_other_deg 1.136 r_chiral_restr 0.117 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4217 Nucleic Acid Atoms Solvent Atoms 296 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing