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factor Xa in complex with the dual thrombin-FXa inhibitor 58.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE FACTOR XA STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.7 PROTEIN SOLUTION: 8 MG/ML DESGLA FACTOR XA, 5 MM MES (PH 6.0), 5 MM CACL2, 100 MM BENZAMIDINE. RESERVOIR SOLUTION: 18-20% PEG600, 50 MM MES (PH 5.7). HANGING DROP SETUP.
Crystal Properties Matthews coefficient Solvent content 2.4 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.65 α = 90 b = 55.65 β = 90 c = 173.16 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2007-04-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.29 47.98 98.5 0.14 6.7 2.9 26327 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.36 94.7 0.51 2.6 2.5
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 IN-HOUSE FACTOR XA STRUCTURE 2.3 36.99 25117 1207 98.46 0.16862 0.166 0.181 0.22434 0.2284 RANDOM
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 14.801 r_dihedral_angle_3_deg 14.285 r_dihedral_angle_1_deg 5.467 r_angle_refined_deg 1.051 r_angle_other_deg 0.796 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.436 r_dihedral_angle_4_deg 14.801 r_dihedral_angle_3_deg 14.285 r_dihedral_angle_1_deg 5.467 r_angle_refined_deg 1.051 r_angle_other_deg 0.796 r_chiral_restr 0.058 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 r_bond_other_d 0.002 r_gen_planes_other 0.001 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_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined 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 4498 Nucleic Acid Atoms Solvent Atoms 609 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling