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Protein kinase Pim-1 in complex with fragment-1 from crystallographic fragment screen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE PIM STRUCTURE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.9 M (NH4)2HPO4, 0.1 M SODIUM CITRATE PH=5.5, 0.2M NACL
Crystal Properties Matthews coefficient Solvent content 3.28 62.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.802 α = 90 b = 96.802 β = 90 c = 80.595 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 100 CCD MARRESEARCH 2008-05-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 BESSY 14.2
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 2.4 42.1 91.2 0.1 17.2 6.9 15473
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 2.4 2.49 51.2 0.44 2.1 3.8
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 PIM STRUCTURE 2.4 42.11 14680 780 91.29 0.17279 0.17058 0.1735 0.21394 0.2133 RANDOM 22.033
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] -0.3 -0.15 -0.3 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.693 r_dihedral_angle_4_deg 18.581 r_dihedral_angle_3_deg 15.971 r_scangle_it 7.555 r_dihedral_angle_1_deg 6.432 r_scbond_it 5.677 r_mcangle_it 3.657 r_mcbond_it 2.306 r_angle_refined_deg 1.415 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.693 r_dihedral_angle_4_deg 18.581 r_dihedral_angle_3_deg 15.971 r_scangle_it 7.555 r_dihedral_angle_1_deg 6.432 r_scbond_it 5.677 r_mcangle_it 3.657 r_mcbond_it 2.306 r_angle_refined_deg 1.415 r_nbtor_refined 0.302 r_nbd_refined 0.197 r_xyhbond_nbd_refined 0.141 r_symmetry_vdw_refined 0.131 r_chiral_restr 0.097 r_symmetry_hbond_refined 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.005 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 2238 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing