☰ Navigation Tabs
mPI3Kd in complex with an inhibitor
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 293 ethylene glycol per PEG 8000, carboxylic acids mix, buffer system 2,
Crystal Properties Matthews coefficient Solvent content 2.09 41.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.805 α = 90 b = 64.839 β = 103.655 c = 116.582 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 2014-03-10 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) 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 1.72 113.29 99.4 0.079 8.9 3.4 107997
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 1.72 1.89 0.79
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 42.965 94732 4709 99.244 0.238 0.2363 0.2407 0.2756 0.2788 35.419
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] 0.043 0.049 -0.349 0.252
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.696 r_dihedral_angle_4_deg 16.735 r_dihedral_angle_3_deg 15.176 r_lrange_it 7.634 r_lrange_other 7.634 r_dihedral_angle_1_deg 6.237 r_scangle_it 5.312 r_scangle_other 5.311 r_mcangle_it 4.228 r_mcangle_other 4.228
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.696 r_dihedral_angle_4_deg 16.735 r_dihedral_angle_3_deg 15.176 r_lrange_it 7.634 r_lrange_other 7.634 r_dihedral_angle_1_deg 6.237 r_scangle_it 5.312 r_scangle_other 5.311 r_mcangle_it 4.228 r_mcangle_other 4.228 r_scbond_it 3.427 r_scbond_other 3.427 r_mcbond_other 3.001 r_mcbond_it 3 r_angle_refined_deg 1.516 r_angle_other_deg 1.292 r_symmetry_nbd_refined 0.333 r_nbd_refined 0.212 r_symmetry_xyhbond_nbd_other 0.199 r_symmetry_xyhbond_nbd_refined 0.195 r_nbd_other 0.187 r_symmetry_nbd_other 0.18 r_nbtor_refined 0.168 r_xyhbond_nbd_refined 0.148 r_symmetry_nbtor_other 0.079 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 257 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing