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Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with monoaryl P4 motifs
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZQ PDB ENTRY 1EZQ
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% PEG6K, 50MM MES-NAOH (PH5.5-6), 5MM CACL2 AND 50MM NACL., pH 5.75
Crystal Properties Matthews coefficient Solvent content 1.85 33.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.673 α = 90 b = 72.814 β = 90 c = 78.509 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 CCD 2003-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.88 30 99.2 0.09 21.6 7.26 26765
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 1.88 1.97 98.6 0.57 4 7.1
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1EZQ 1.88 29.49 25362 1346 100 0.19759 0.19566 0.1971 0.23446 RANDOM 30.686
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] 0.1 -1.44 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.926 r_dihedral_angle_4_deg 10.874 r_dihedral_angle_3_deg 10.345 r_scangle_it 5.617 r_dihedral_angle_1_deg 4.05 r_scbond_it 3.579 r_mcangle_it 2.711 r_angle_refined_deg 1.462 r_mcbond_it 1.415 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.926 r_dihedral_angle_4_deg 10.874 r_dihedral_angle_3_deg 10.345 r_scangle_it 5.617 r_dihedral_angle_1_deg 4.05 r_scbond_it 3.579 r_mcangle_it 2.711 r_angle_refined_deg 1.462 r_mcbond_it 1.415 r_chiral_restr 0.096 r_bond_refined_d 0.011 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 2182 Nucleic Acid Atoms Solvent Atoms 210 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing