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Crystal structure of the mammalian C2alpha-PI3 Kinase PX-domain
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 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 6.00
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 48.8 99.2 0.057 5.4 16365 41.2
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 1.8 48.8 16345 15519 826 99.2 0.223 0.222 0.2332 0.244 0.261 RANDOM 42.75
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] 0.52 0.26 0.52 -0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 13.55 r_scangle_it 5.969 r_mcangle_it 3.982 r_scbond_it 3.853 r_mcbond_it 2.293 r_angle_refined_deg 1.89 r_angle_other_deg 0.979 r_symmetry_vdw_other 0.352 r_nbd_refined 0.271 r_nbd_other 0.257
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 13.55 r_scangle_it 5.969 r_mcangle_it 3.982 r_scbond_it 3.853 r_mcbond_it 2.293 r_angle_refined_deg 1.89 r_angle_other_deg 0.979 r_symmetry_vdw_other 0.352 r_nbd_refined 0.271 r_nbd_other 0.257 r_symmetry_vdw_refined 0.249 r_xyhbond_nbd_refined 0.177 r_chiral_restr 0.143 r_nbtor_other 0.093 r_symmetry_hbond_refined 0.05 r_bond_refined_d 0.016 r_gen_planes_other 0.016 r_gen_planes_refined 0.015 r_bond_other_d 0.001 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_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 957 Nucleic Acid Atoms Solvent Atoms 92 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling EPMR phasing