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Human PIM1 kinase in complex with compound 12b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.3 293 18% PEG 3350, 0.2 M Na2SO4, 6% ethylene glycol, 0.1 M Tris, pH 7.3
Crystal Properties Matthews coefficient Solvent content 3.46 64.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 97.035 α = 90 b = 97.035 β = 90 c = 81.13 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 ADSC QUANTUM 315r 2010-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9731 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.573 84.035 96.3 0.086 0.091 0.028 21.1 10.2 13375 60.79
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.573 2.581 74.5 0.624 0.661 0.321 2.8 7.2
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 5kgd 2.573 21.78 13324 667 95.82 0.1709 0.1696 0.168 0.1957 0.1821 RANDOM 46.16
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] -2.9045 -2.9045 5.8089
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.24 t_omega_torsion 3.18 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 17.24 t_omega_torsion 3.18 t_angle_deg 1 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2224 Nucleic Acid Atoms Solvent Atoms 83 Heterogen Atoms 54
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing Coot model building