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Crystal structure of proto-oncogene kinase Pim1 bound to hispidulin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2O3P
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 277 1M NaOAc, 0.1M Imidazole
Crystal Properties Matthews coefficient Solvent content 3.38 63.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.999 α = 90 b = 97.999 β = 90 c = 80.599 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 RAYONIX MX300HE 2014-11-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.04 50 100 0.068 9.7 5.7 28099 23.37
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.04 2.11 100 2.1 5.7
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 2O3P 2.04 42.435 25569 1344 95.83 0.20152 0.20026 0.209 0.22574 0.2309 RANDOM 31.325
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] 0.26 0.13 0.26 -0.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_1_deg 5.519 r_long_range_B_refined 5.231 r_long_range_B_other 5.231 r_angle_other_deg 3.543 r_scangle_other 3.503 r_mcangle_it 2.902 r_mcangle_other 2.902
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.834 r_dihedral_angle_4_deg 18.752 r_dihedral_angle_3_deg 14.539 r_dihedral_angle_1_deg 5.519 r_long_range_B_refined 5.231 r_long_range_B_other 5.231 r_angle_other_deg 3.543 r_scangle_other 3.503 r_mcangle_it 2.902 r_mcangle_other 2.902 r_scbond_it 2.111 r_scbond_other 2.11 r_mcbond_it 1.782 r_mcbond_other 1.778 r_angle_refined_deg 1.346 r_chiral_restr 0.096 r_gen_planes_other 0.026 r_gen_planes_refined 0.015 r_bond_refined_d 0.01 r_bond_other_d 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2224 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 22
Software Software Software Name Purpose REFMAC refinement Coot model building HKL-2000 data processing