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Human diphosphoinositol polyphosphate phosphohydrolase 1, Mg-F complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FVV PDB entry 2FVV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 277 30% PEG 8000, 200 mM LiCl, 5 mM MgCl2, 20 mM NaF, 5 mM IP6, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.9 35.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.193 α = 90 b = 59.444 β = 90 c = 62.547 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 100 CCD Bruker Platinum 135 Helios multilayer mirrors 2007-05-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR
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 1.65 50 99.8 0.054 11.7 2.1 20890 20848 -3
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) 1.65 1.75 99.3 0.461 2.1
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2FVV 1.65 32.21 20848 20813 1067 99.7 0.194 0.194 0.192 0.1969 0.23 0.2342 RANDOM 15.789
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] 0.02 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.112 r_dihedral_angle_4_deg 20.631 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 6.861 r_scangle_it 4.469 r_scbond_it 3.211 r_angle_refined_deg 1.846 r_mcangle_it 1.761 r_mcbond_it 1.591 r_angle_other_deg 1.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.112 r_dihedral_angle_4_deg 20.631 r_dihedral_angle_3_deg 13.81 r_dihedral_angle_1_deg 6.861 r_scangle_it 4.469 r_scbond_it 3.211 r_angle_refined_deg 1.846 r_mcangle_it 1.761 r_mcbond_it 1.591 r_angle_other_deg 1.001 r_mcbond_other 0.357 r_nbd_other 0.215 r_nbd_refined 0.212 r_metal_ion_refined 0.188 r_xyhbond_nbd_refined 0.183 r_symmetry_vdw_other 0.18 r_nbtor_refined 0.173 r_symmetry_hbond_refined 0.157 r_chiral_restr 0.122 r_nbtor_other 0.094 r_symmetry_vdw_refined 0.084 r_xyhbond_nbd_other 0.027 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_gen_planes_other 0.003 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1110 Nucleic Acid Atoms Solvent Atoms 146 Heterogen Atoms 87
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction PROTEUM PLUS data collection SAINT data reduction SADABS data scaling REFMAC phasing