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Human Thrombopoietin Functional Domain Complexed To Neutralizing Antibody TN1 Fab
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IAI PDB ENTRY 1IAI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20% PEG 4000, 0.1M potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.29 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.099 α = 90 b = 46.771 β = 90.48 c = 185.151 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 MARRESEARCH 1999-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
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 2.5 60 92 0.074 8.1 2.6 36766 -1 48.9
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) 2.5 2.59 71 0.318 1.1 1.6 2814
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 PDB ENTRY 1IAI 2.51 45.28 34911 1852 92.87 0.23185 0.22751 0.2295 0.31579 0.3149 RANDOM 49.886
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] -0.08 0.48 0.05 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.937 r_scangle_it 3.767 r_scbond_it 2.343 r_angle_refined_deg 2.008 r_mcangle_it 1.635 r_mcbond_it 0.871 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.272 r_xyhbond_nbd_refined 0.22 r_symmetry_hbond_refined 0.186
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.937 r_scangle_it 3.767 r_scbond_it 2.343 r_angle_refined_deg 2.008 r_mcangle_it 1.635 r_mcbond_it 0.871 r_symmetry_vdw_refined 0.286 r_nbd_refined 0.272 r_xyhbond_nbd_refined 0.22 r_symmetry_hbond_refined 0.186 r_chiral_restr 0.126 r_bond_refined_d 0.02 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_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 8746 Nucleic Acid Atoms Solvent Atoms 156 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing