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HUMAN PI3KDELTA IN COMPLEX WITH COMPOUND 3C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously derived model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 293 12-14% PEG6000, 100 MM MES/NAOH, PH 5.75, 5 MM DTT
Crystal Properties Matthews coefficient Solvent content 2.7 53.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.284 α = 90 b = 109.308 β = 90 c = 142.579 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2013-11-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.99998 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) Rrim 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 2.79 86.75 100 0.058 0.066 5.5 8.3 36279
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.79 3.01 99.9 0.589 0.673 1.3 8.2
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 FOURIER SYNTHESIS THROUGHOUT previously derived model 2.79 86.75 35462 739 99.97 0.2415 0.2405 0.2326 0.2895 0.2799 RANDOM 97.127
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] 0.64 1.81 -2.45
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.314 r_dihedral_angle_4_deg 13.153 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_1_deg 5.389 r_angle_other_deg 1.272 r_angle_refined_deg 1.042 r_nbd_refined 0.161 r_nbtor_refined 0.155 r_nbd_other 0.136 r_symmetry_hbond_refined 0.132
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.314 r_dihedral_angle_4_deg 13.153 r_dihedral_angle_3_deg 12.816 r_dihedral_angle_1_deg 5.389 r_angle_other_deg 1.272 r_angle_refined_deg 1.042 r_nbd_refined 0.161 r_nbtor_refined 0.155 r_nbd_other 0.136 r_symmetry_hbond_refined 0.132 r_symmetry_vdw_other 0.108 r_symmetry_vdw_refined 0.093 r_xyhbond_nbd_refined 0.074 r_nbtor_other 0.068 r_chiral_restr 0.058 r_bond_refined_d 0.008 r_bond_other_d 0.002 r_gen_planes_refined 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9029 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PDB_EXTRACT data extraction