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Benzofuropyrimidinone Inhibitors of Pim-1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE PIM1 STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.2 pH 7.2
Crystal Properties Matthews coefficient Solvent content 2.9 64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.449 α = 90 b = 97.449 β = 90 c = 81.003 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 155 CCD MARMOSAIC 325 mm CCD 2007-01-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
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 1.92 37.42 97.9 0.07 17.33 7.4 33275 -3
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 1.92 2.03 95.2 1.28 1.6 5.92
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN-HOUSE PIM1 STRUCTURE 1.92 37.42 31220 1670 98.32 0.15781 0.15516 0.154 0.20731 0.2053 RANDOM 37.685
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 17.316 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_1_deg 6.771 r_scangle_it 6.036 r_scbond_it 4.345 r_mcangle_it 2.715 r_angle_refined_deg 2.238 r_mcbond_it 1.845 r_nbtor_refined 0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 17.316 r_dihedral_angle_3_deg 13.795 r_dihedral_angle_1_deg 6.771 r_scangle_it 6.036 r_scbond_it 4.345 r_mcangle_it 2.715 r_angle_refined_deg 2.238 r_mcbond_it 1.845 r_nbtor_refined 0.32 r_symmetry_hbond_refined 0.278 r_nbd_refined 0.236 r_xyhbond_nbd_refined 0.231 r_symmetry_vdw_refined 0.213 r_chiral_restr 0.191 r_bond_refined_d 0.031 r_gen_planes_refined 0.012 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 2223 Nucleic Acid Atoms Solvent Atoms 337 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing