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Hemostatic effect of a monoclonal antibody mAb 2021 blocking the interaction between FXa and TFPI in a rabbit hemophilia model
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F8T PDB ENTRIES 1F8T AND 1TFX experimental model PDB 1TFX PDB ENTRIES 1F8T AND 1TFX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 295 0.05 M CALCIUM CHLORIDE, 0.1 M MES, pH 6.0, 45% V/V PEG 200, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.72 66.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.01 α = 90 b = 125.64 β = 90 c = 202.34 γ = 90
Symmetry Space Group I 2 2 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 TWO MIRRORS 2009-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-3 MAX II I911-3
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 1.8 30 99 0.066 12.7 4.8 76298 -3 36
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 98.5 2
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 ENTRIES 1F8T AND 1TFX 1.8 29.102 77080 72056 3817 98.43 0.19789 0.19585 0.195 0.23637 0.2347 RANDOM 39.36
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] -12.23 17.85 -5.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_4_deg 22.357 r_dihedral_angle_3_deg 14.306 r_dihedral_angle_1_deg 7.723 r_angle_refined_deg 2.682 r_chiral_restr 0.191 r_bond_refined_d 0.029 r_gen_planes_refined 0.017 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.737 r_dihedral_angle_4_deg 22.357 r_dihedral_angle_3_deg 14.306 r_dihedral_angle_1_deg 7.723 r_angle_refined_deg 2.682 r_chiral_restr 0.191 r_bond_refined_d 0.029 r_gen_planes_refined 0.017 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_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3827 Nucleic Acid Atoms Solvent Atoms 400 Heterogen Atoms 102
Software Software Software Name Purpose MxCuBE data collection PHASER phasing REFMAC refinement XDS data reduction XSCALE data scaling