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mPI3Kd in complex with compound 12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other Internal Model
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 ethylene glycol per PEG 8000, carboxylic acids mix, buffer system 2,
Crystal Properties Matthews coefficient Solvent content 2.09 41.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.847 α = 90 b = 65.161 β = 103.752 c = 116.426 γ = 90
Symmetry Space Group C 1 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 100 PIXEL DECTRIS PILATUS 300K 2014-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 0.9724 ESRF ID23-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.8 113.09 97.6 0.054 0.064 14.4 3.5 93293
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 1.83 0.374
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE Internal Model 1.8 113.089 93293 4789 97.363 0.228 0.2265 0.2312 0.2626 0.2686 40.747
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] 0.489 -0.504 1.399 -1.466
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.136 r_dihedral_angle_4_deg 18.648 r_dihedral_angle_3_deg 14.86 r_lrange_other 9.098 r_lrange_it 9.074 r_scangle_other 6.614 r_scangle_it 6.589 r_dihedral_angle_1_deg 6.429 r_mcangle_it 4.951 r_mcangle_other 4.951
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.136 r_dihedral_angle_4_deg 18.648 r_dihedral_angle_3_deg 14.86 r_lrange_other 9.098 r_lrange_it 9.074 r_scangle_other 6.614 r_scangle_it 6.589 r_dihedral_angle_1_deg 6.429 r_mcangle_it 4.951 r_mcangle_other 4.951 r_scbond_other 4.423 r_scbond_it 4.41 r_mcbond_other 3.731 r_mcbond_it 3.73 r_angle_refined_deg 1.598 r_angle_other_deg 1.33 r_symmetry_nbd_refined 0.346 r_nbd_refined 0.218 r_symmetry_xyhbond_nbd_refined 0.208 r_nbd_other 0.189 r_symmetry_nbd_other 0.183 r_nbtor_refined 0.17 r_xyhbond_nbd_refined 0.169 r_symmetry_xyhbond_nbd_other 0.136 r_chiral_restr 0.083 r_symmetry_nbtor_other 0.079 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6675 Nucleic Acid Atoms Solvent Atoms 365 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing