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Crystal structure of the catalytic domain of human inositol 1,4,5-trisphosphate 3-kinase C
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1W2C PDB Entry 1w2c
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 298 PEG3350, Sodium thiocyanate, Magnesium chloride, inositol 1,4,5-trisphosphate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.5 50
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.72 α = 90 b = 87.72 β = 90 c = 174.94 γ = 120
Symmetry Space Group P 61 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 AREA DETECTOR MARRESEARCH 2005-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.9537 BESSY 14.1
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 2.6 28.68 97.6 0.075 21.79 12906 12906 1 1
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 2.6 2.65 99.7 86.1 0.634 3.7
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 (All) 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 1w2c 2.6 28.68 13501 12872 629 99.9 0.22 0.22 0.218 0.2082 0.262 0.2525 RANDOM 32.726
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] 0.29 0.15 0.29 -0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_dihedral_angle_3_deg 20.941 r_dihedral_angle_4_deg 18.701 r_dihedral_angle_1_deg 9.864 r_scangle_it 2.488 r_angle_refined_deg 1.849 r_scbond_it 1.682 r_mcangle_it 0.956 r_mcbond_it 0.574 r_nbtor_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.676 r_dihedral_angle_3_deg 20.941 r_dihedral_angle_4_deg 18.701 r_dihedral_angle_1_deg 9.864 r_scangle_it 2.488 r_angle_refined_deg 1.849 r_scbond_it 1.682 r_mcangle_it 0.956 r_mcbond_it 0.574 r_nbtor_refined 0.316 r_symmetry_vdw_refined 0.261 r_nbd_refined 0.241 r_chiral_restr 0.179 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.078 r_bond_refined_d 0.019 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2075 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 24
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection PHASER phasing