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Structure of Anticalin N7E in complex with the three-domain fragment Fn7B8 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 5.5 298 17 % (w/v) PEG3350, 0.2 M NaCl, 0.1 M Na-malonate
Crystal Properties Matthews coefficient Solvent content 2.95 58.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.148 α = 90 b = 135.148 β = 90 c = 203.939 γ = 90
Symmetry Space Group P 41 21 2
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 2012-07-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 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 3 35 99.9 0.124 0.129 0.999 21.7 14.67 38486 -3 63.078
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 3 3.1 100 1.059 1.096 0.888 3.08 15.065
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 3 35 36560 1926 99.86 0.2096 0.208 0.206 0.241 0.2368 RANDOM 97.772
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] 2.44 2.44 -4.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.809 r_dihedral_angle_4_deg 18.489 r_dihedral_angle_3_deg 14.894 r_dihedral_angle_1_deg 6.342 r_angle_refined_deg 1.308 r_angle_other_deg 0.886 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.809 r_dihedral_angle_4_deg 18.489 r_dihedral_angle_3_deg 14.894 r_dihedral_angle_1_deg 6.342 r_angle_refined_deg 1.308 r_angle_other_deg 0.886 r_chiral_restr 0.078 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9943 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing