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Protein kinase Pim-1 in complex with fragment-2 from crystallographic fragment screen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN-HOUSE PIM-1 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 = 96.987 α = 90 b = 96.987 β = 90 c = 80.87 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 2.2 48.6 96 0.09 21.2 8.6 21175
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 2.2 2.28 71.3 0.45 2.25 4.8
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-1 STRUCTURE 2.2 48.62 20074 1065 95.97 0.1715 0.16994 0.1732 0.20075 0.2018 RANDOM 18.238
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] -0.5 -0.25 -0.5 0.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 14.985 r_scangle_it 6.381 r_dihedral_angle_1_deg 5.742 r_scbond_it 4.709 r_mcangle_it 2.815 r_mcbond_it 1.904 r_angle_refined_deg 1.214 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.818 r_dihedral_angle_4_deg 17.42 r_dihedral_angle_3_deg 14.985 r_scangle_it 6.381 r_dihedral_angle_1_deg 5.742 r_scbond_it 4.709 r_mcangle_it 2.815 r_mcbond_it 1.904 r_angle_refined_deg 1.214 r_nbtor_refined 0.304 r_nbd_refined 0.187 r_symmetry_vdw_refined 0.151 r_xyhbond_nbd_refined 0.142 r_symmetry_hbond_refined 0.108 r_chiral_restr 0.08 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 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 2234 Nucleic Acid Atoms Solvent Atoms 132 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing