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Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-yl)sulfonyl]piperazin-1-yl] carbonyl]thieno[3,2-b]pyridine n-oxide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FAX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SEEDING 5 293 pH 5.00, VAPOR DIFFUSION, SEEDING, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.078 α = 90 b = 73.122 β = 90 c = 79.949 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 300 IMAGE PLATE RIGAKU RAXIS IIC monochromator 2000-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.2 33.25 97.3 0.055 0.055 14.6 3.57 17081 17081
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 95.8 0.305 0.305 4.2 3.62 1662
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION RIGID BODY REFINEMENT THROUGHOUT 1FAX 2.2 25 16215 857 100 0.18799 0.18556 0.23219 RANDOM 38.058
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] 0.27 -0.8 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.152 r_dihedral_angle_4_deg 25.678 r_dihedral_angle_3_deg 15.575 r_dihedral_angle_1_deg 6.59 r_scangle_it 3.724 r_mcangle_it 3.096 r_scbond_it 2.552 r_angle_refined_deg 1.953 r_mcbond_it 1.919 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.152 r_dihedral_angle_4_deg 25.678 r_dihedral_angle_3_deg 15.575 r_dihedral_angle_1_deg 6.59 r_scangle_it 3.724 r_mcangle_it 3.096 r_scbond_it 2.552 r_angle_refined_deg 1.953 r_mcbond_it 1.919 r_nbtor_refined 0.32 r_symmetry_hbond_refined 0.229 r_metal_ion_refined 0.224 r_nbd_refined 0.222 r_symmetry_vdw_refined 0.208 r_xyhbond_nbd_refined 0.18 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2149 Nucleic Acid Atoms Solvent Atoms 111 Heterogen Atoms 33
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction REFMAC refinement