☰ Navigation Tabs
myo-inositol 3-kinase bound with its substrates (AMPPCP and myo-inositol)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3W4S
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 PEG 3350, NH4I
Crystal Properties Matthews coefficient Solvent content 2.09 41.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.134 α = 90 b = 81.176 β = 90 c = 81.109 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 95 CCD ADSC QUANTUM 270 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NE3A 1.0000 Photon Factory AR-NE3A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.93 50 99.7 0.07 26.3 7.1 38880
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3W4S 1.93 36.32 36873 1956 99.56 0.2178 0.2159 0.2546 0.2949 RANDOM 35.404
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] -0.71 -1.85 2.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 21.987 r_dihedral_angle_3_deg 14.749 r_dihedral_angle_1_deg 6.623 r_angle_refined_deg 1.503 r_angle_other_deg 0.926 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.12 r_dihedral_angle_4_deg 21.987 r_dihedral_angle_3_deg 14.749 r_dihedral_angle_1_deg 6.623 r_angle_refined_deg 1.503 r_angle_other_deg 0.926 r_chiral_restr 0.095 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4147 Nucleic Acid Atoms Solvent Atoms 105 Heterogen Atoms 110
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data scaling REFMAC phasing