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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, HANGING DROP 5.75 CRYSTALLISATION WAS CARRIED OUT USING HANG DROP VAPOUR DIFFUSION METHODS IN 2UL DROPS CONTAINING 1:1 RATIO 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 1.83 32.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.564 α = 90 b = 72.485 β = 90 c = 78.177 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 2.38 30 98.2 0.06 22.7 4.3 13086
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 2.38 2.49 96.4 0.37 4 4
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 2.38 28.4 12423 637 100 0.19979 0.19692 0.1995 0.25478 RANDOM 51.775
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] -0.86 -2.39 3.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.678 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_3_deg 11.453 r_scangle_it 5.358 r_dihedral_angle_1_deg 3.671 r_scbond_it 3.469 r_mcangle_it 2.741 r_angle_refined_deg 1.525 r_mcbond_it 1.377 r_chiral_restr 0.108
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.678 r_dihedral_angle_4_deg 15.896 r_dihedral_angle_3_deg 11.453 r_scangle_it 5.358 r_dihedral_angle_1_deg 3.671 r_scbond_it 3.469 r_mcangle_it 2.741 r_angle_refined_deg 1.525 r_mcbond_it 1.377 r_chiral_restr 0.108 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 2204 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing