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CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AFTER ADDITION OF INOSITOL 1,3,4-TRISPHOSPHATE AT 2.5 ANGSTROM RESOLUTION
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1INP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.25 293 -Mg2+/-Li+/+Ins(1,3,4)P3/+Gd3+ (data=ip1r): Reservoir solution consisted of 10% PEG 8000, 80mM Bis-Tris, pH 5.25, 2mM Gd2(SO4)3, 1mM Ins(1,3,4)P3
Crystal Properties Matthews coefficient Solvent content 2.17 43.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.64 α = 90 b = 51.64 β = 90 c = 143.33 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 296 AREA DETECTOR UCSD MARK II 1994-07-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.542
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 2.8 6.95 79 0.061 4.2 1.5 15787
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 3.02 70 0.127
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 FOURIER SYNTHESIS THROUGHOUT 1INP 2.8 6.95 7291 431 83.37 0.20742 0.20482 0.2065 0.25027 0.2497 RANDOM 20.325
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] 0.66 0.66 -1.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_4_deg 8.55 r_dihedral_angle_1_deg 6.095 r_long_range_B_refined 3.132 r_long_range_B_other 3.104 r_mcangle_it 1.659 r_mcangle_other 1.659 r_scangle_other 1.207 r_angle_refined_deg 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.321 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_4_deg 8.55 r_dihedral_angle_1_deg 6.095 r_long_range_B_refined 3.132 r_long_range_B_other 3.104 r_mcangle_it 1.659 r_mcangle_other 1.659 r_scangle_other 1.207 r_angle_refined_deg 1.041 r_angle_other_deg 0.993 r_mcbond_it 0.909 r_mcbond_other 0.907 r_scbond_other 0.662 r_scbond_it 0.661 r_chiral_restr 0.027 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.004 r_gen_planes_other 0.004 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2521 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement UCSD-system data reduction UCSD-system data scaling SQUASH phasing