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Crystal structures of C2ALPHA-PI3 kinase PX-domain domain indicate conformational change associated with ligand binding.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OCS PDB entry 1OCS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 293 0.1M MALEIC ACID/NAOH, 10% GLYCEROL, PH 6.00, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
Crystal Properties Matthews coefficient Solvent content 2.85 56.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.554 α = 90 b = 56.554 β = 90 c = 92.894 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 98 CCD ADSC QUANTUM 4 2004-11-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.8 30 99.2 0.057 5.4 9942
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 1.8 1.86 99.9 0.49 2.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1OCS 2.1 28.27 9844 9844 539 98.87 0.23763 0.23542 0.2243 0.27417 0.2618 RANDOM 35.623
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] 0.45 0.22 0.45 -0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 18.723 r_dihedral_angle_3_deg 18.59 r_dihedral_angle_1_deg 8.099 r_scangle_it 4.683 r_scbond_it 3.364 r_mcangle_it 3.015 r_mcbond_it 2.186 r_angle_refined_deg 1.782 r_nbtor_refined 0.319
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.482 r_dihedral_angle_4_deg 18.723 r_dihedral_angle_3_deg 18.59 r_dihedral_angle_1_deg 8.099 r_scangle_it 4.683 r_scbond_it 3.364 r_mcangle_it 3.015 r_mcbond_it 2.186 r_angle_refined_deg 1.782 r_nbtor_refined 0.319 r_symmetry_vdw_refined 0.254 r_nbd_refined 0.23 r_xyhbond_nbd_refined 0.212 r_symmetry_hbond_refined 0.154 r_chiral_restr 0.139 r_bond_refined_d 0.021 r_gen_planes_refined 0.009 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 935 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement ADSC data collection DENZO data reduction SCALEPACK data scaling EPMR phasing