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Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with biaryl P4 motifs
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.85 CRYSTALLISATION WAS CARRIED OUT USING THE HANGING DROP VAPOUR DIFFUSION METHOD IN 2UL DROPS CONTAINING A 1:1 MIXTURE OF PROTEIN AND WELL SOLUTION. WELL SOLUTION CONTAINED 16-20% PEG 6K, 50MM MES-NAOH (PH5.7-6.0), 5MM CACL2 AND 50MM NACL, pH 5.85
Crystal Properties Matthews coefficient Solvent content 1.83 32.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.959 α = 90 b = 72.309 β = 90 c = 78.976 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 2002-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX14.2 SRS PX14.2
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 1.93 25 93.1 0.05 3.6 22951
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 1.95 2.02 0.45
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MOLECULAR REPLACEMENT THROUGHOUT 1.95 20 21412 1159 100 0.19906 0.19676 0.24163 RANDOM 36.992
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] 1.14 -1.84 0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.106 r_dihedral_angle_4_deg 21.075 r_dihedral_angle_3_deg 12.069 r_scangle_it 5.457 r_dihedral_angle_1_deg 3.948 r_scbond_it 3.716 r_mcangle_it 2.936 r_mcbond_it 1.721 r_angle_refined_deg 1.625 r_nbtor_refined 0.309
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.106 r_dihedral_angle_4_deg 21.075 r_dihedral_angle_3_deg 12.069 r_scangle_it 5.457 r_dihedral_angle_1_deg 3.948 r_scbond_it 3.716 r_mcangle_it 2.936 r_mcbond_it 1.721 r_angle_refined_deg 1.625 r_nbtor_refined 0.309 r_symmetry_hbond_refined 0.21 r_nbd_refined 0.203 r_xyhbond_nbd_refined 0.189 r_symmetry_vdw_refined 0.186 r_chiral_restr 0.111 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 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_refined r_metal_ion_other r_symmetry_vdw_other 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 2227 Nucleic Acid Atoms Solvent Atoms 171 Heterogen Atoms 35
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling REFMAC phasing