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Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)sulfonyl]-2-(2-methylpropyl)-1-[[5-(pyridin-4-yl) pyrimidin-2-yl]carbonyl]piperazine
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, HANGING DROP 5 293 PEG6000, NaAcetate, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.2 44.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.569 α = 90 b = 72.487 β = 90 c = 79.02 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 293 IMAGE PLATE RIGAKU RAXIS IIC 1999-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.542
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 2.3 39.51 90.6 0.064 0.338 11.7 2.9 13656
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) 1 2.3 2.38 84.3 0.338 0.338 2.89 2.89
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 2.3 25 12933 697 100 0.1913 0.18871 0.23535 RANDOM 45.3
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] 0.31 -1.7 1.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.164 r_dihedral_angle_4_deg 30.158 r_dihedral_angle_3_deg 18.214 r_dihedral_angle_1_deg 7.279 r_scangle_it 3.961 r_mcangle_it 3.175 r_scbond_it 2.648 r_angle_refined_deg 2.116 r_mcbond_it 1.93 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.164 r_dihedral_angle_4_deg 30.158 r_dihedral_angle_3_deg 18.214 r_dihedral_angle_1_deg 7.279 r_scangle_it 3.961 r_mcangle_it 3.175 r_scbond_it 2.648 r_angle_refined_deg 2.116 r_mcbond_it 1.93 r_nbtor_refined 0.328 r_nbd_refined 0.25 r_metal_ion_refined 0.215 r_symmetry_vdw_refined 0.211 r_xyhbond_nbd_refined 0.183 r_symmetry_hbond_refined 0.149 r_chiral_restr 0.13 r_bond_refined_d 0.022 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other 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 2155 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 35
Software Software Software Name Purpose d*TREK data scaling d*TREK data reduction REFMAC refinement