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The crystal structure of the kinase domain of the protein kinase C theta in complex with NVP-XAA228 at 2.32A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FOT PDB ENTRY 1FOT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 VAPOR DIFFUSION AT 4C PROTEIN SOLUTION: 10MG/ML PROTEIN IN 0.2M NACL, 0.05M IMIDAZOLE, 0.001M NAF, 0.05M TCEP, PH = 8.0 RESERVOIR SOLUTION: 0.1 M NA-CACODYLATE PH = 6.5 24% MPD (V/V) 4% PEG8000 (W/V) DROP: 1:1 SMALL ORGANIC MOLECULES LIKE 2,5-HEXANEDIOL AND SULFOBETAINE-195 HAVE A POSITIVE EFFECT ON THE CRYSTAL GROWTH
Crystal Properties Matthews coefficient Solvent content 3.14 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.172 α = 90 b = 152.172 β = 90 c = 74.837 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 2002-09-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA SLS X06SA
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 2.32 50 99.7 0.06 10.4 4.8 42831
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 2.32 2.36 100 0.48
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 PDB ENTRY 1FOT 2.32 19.88 40693 2131 100 0.188 0.186 0.2266 0.221 0.2552 RANDOM 49.2
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] -0.17 -0.08 -0.17 0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_dihedral_angle_4_deg 17.011 r_dihedral_angle_3_deg 17.001 r_dihedral_angle_1_deg 7.128 r_scangle_it 2.847 r_scbond_it 1.861 r_angle_refined_deg 1.445 r_mcangle_it 1.222 r_mcbond_it 0.734 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_dihedral_angle_4_deg 17.011 r_dihedral_angle_3_deg 17.001 r_dihedral_angle_1_deg 7.128 r_scangle_it 2.847 r_scbond_it 1.861 r_angle_refined_deg 1.445 r_mcangle_it 1.222 r_mcbond_it 0.734 r_nbtor_refined 0.303 r_symmetry_hbond_refined 0.233 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.198 r_xyhbond_nbd_refined 0.148 r_chiral_restr 0.109 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 5396 Nucleic Acid Atoms Solvent Atoms 412 Heterogen Atoms 76
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing