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Crystal Structure of INPP5B in complex with phosphatidylinositol 4-phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I9Y PDB ENTRY 1I9Y
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 22% polyacrylic acid, 0.02M magnesium chloride, 0.1M hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 5.51 77.67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.761 α = 90 b = 133.761 β = 90 c = 133.761 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r mirrors 2009-12-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.97908 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.4 94.51 99.8 0.091 0.091 11.1 4.8 31433 31380 54
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 99.9 0.698 0.698 2 4.5 4498
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1I9Y 2.4 47.29 29805 1580 99.88 0.17234 0.17062 0.1783 0.20544 0.2109 RANDOM 43.796
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.448 r_dihedral_angle_4_deg 17.662 r_dihedral_angle_3_deg 13.877 r_dihedral_angle_1_deg 6.384 r_scangle_it 2.881 r_scbond_it 1.736 r_mcangle_it 1.281 r_angle_refined_deg 1.278 r_angle_other_deg 0.806 r_mcbond_it 0.652
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.448 r_dihedral_angle_4_deg 17.662 r_dihedral_angle_3_deg 13.877 r_dihedral_angle_1_deg 6.384 r_scangle_it 2.881 r_scbond_it 1.736 r_mcangle_it 1.281 r_angle_refined_deg 1.278 r_angle_other_deg 0.806 r_mcbond_it 0.652 r_mcbond_other 0.097 r_chiral_restr 0.078 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2510 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 62
Software Software Software Name Purpose ADSC data collection PHASER phasing REFMAC refinement XDS data reduction SCALA data scaling