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Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.75 CRYSTALLISATION WAS CARRIED OUT USING VAPOUR DIFFUSION IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50 MM MES-NAOH (PH 5.5-6), 5 MM CACL2 AND 50 MM NACL.
Crystal Properties Matthews coefficient Solvent content 2.29 45.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.727 α = 90 b = 72.012 β = 90 c = 78.689 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 100 CCD ADSC QUANTUM 4 2004-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-D APS 14-BM-D
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 1.9 25 99.8 0.06 20.91 5.3 25983 23.477
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 1.9 1.93 99.8 0.44 3.19 5.1
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 Selection Details Mean Isotropic B X-RAY DIFFRACTION OTHER THROUGHOUT NONE 1.9 20 24614 1318 100 0.1916 0.18897 0.1924 0.24123 RANDOM 28.508
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] 0.52 -1.36 0.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.705 r_dihedral_angle_4_deg 16.506 r_dihedral_angle_3_deg 10.119 r_scangle_it 4.7 r_dihedral_angle_1_deg 3.766 r_scbond_it 3.005 r_mcangle_it 2.37 r_angle_refined_deg 1.395 r_mcbond_it 1.223 r_chiral_restr 0.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.705 r_dihedral_angle_4_deg 16.506 r_dihedral_angle_3_deg 10.119 r_scangle_it 4.7 r_dihedral_angle_1_deg 3.766 r_scbond_it 3.005 r_mcangle_it 2.37 r_angle_refined_deg 1.395 r_mcbond_it 1.223 r_chiral_restr 0.1 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_other r_mcangle_other r_scbond_other 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 2228 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling