☰ Navigation Tabs
CRYSTAL STRUCTURE OF INOSITOL POLYPHOSPHATE 1-PHOSPHATASE INPP1 IN COMPLEX GADOLINIUM AND LITHIUM 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 6.3 293 13% PEG8000, 200mM Li2SO4 and 100mM Tris, pH 6.3. Upon reaching maximum size after ~5 days, a Gd3+ heavy atom derivative was prepared by adding 0.5uL of 17.5mM Gd2(SO4)3 in reservoir solution to 3uL hanging drops (2.5mM final Gd3+) containing native crystals for 48 hours
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 1992-07-10 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 2.5 15.45 96 0.051 10.8 3.4 26197
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 2.5 2.69 95.6 0.172
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 1INP 2.5 15.45 11645 725 99.98 0.16537 0.16286 0.20497 0.2203 RANDOM 32.228
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] 0.78 0.78 -1.56
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.225 r_dihedral_angle_3_deg 15.766 r_dihedral_angle_4_deg 13.114 r_dihedral_angle_1_deg 5.254 r_scangle_it 1.333 r_angle_refined_deg 1.056 r_scbond_it 0.819 r_mcangle_it 0.748 r_mcbond_it 0.432 r_nbtor_refined 0.296
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.225 r_dihedral_angle_3_deg 15.766 r_dihedral_angle_4_deg 13.114 r_dihedral_angle_1_deg 5.254 r_scangle_it 1.333 r_angle_refined_deg 1.056 r_scbond_it 0.819 r_mcangle_it 0.748 r_mcbond_it 0.432 r_nbtor_refined 0.296 r_symmetry_vdw_refined 0.211 r_nbd_refined 0.181 r_symmetry_hbond_refined 0.138 r_xyhbond_nbd_refined 0.116 r_chiral_restr 0.069 r_metal_ion_refined 0.01 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2532 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement UCSD-system data reduction UCSD-system data scaling SQUASH phasing