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Crystal Structure of INPP5B in complex with Phosphatidylinositol 3,4- bisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N9V PDB ENTRY 3N9V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 1.1 M NA-MALONATE PH 7.0, 0.1 M HEPES PH 7.0, 0.5% JEFFAMINE ED-2001 PH 7.0, 2MM MGSO4, 2MM PTDINS-(3,4,5)-P3 (1,2-DIOCTANOYL)
Crystal Properties Matthews coefficient Solvent content 5.58 77.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 133.661 α = 90 b = 133.661 β = 90 c = 133.661 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 77 CCD MARRESEARCH MIRRORS 2010-04-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I911-2 MAX II I911-2
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 2.3 29.89 99.9 0.09 7.8 5.5 35595 -3
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 2.3 2.42 100 0.65 1.2 5.6
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3N9V 2.3 28.5 33778 1786 99.99 0.17628 0.17506 0.1993 0.1716 RANDOM 27.567
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 32.824 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 13.001 r_dihedral_angle_1_deg 6.342 r_scangle_it 2.351 r_scbond_it 1.422 r_angle_refined_deg 1.243 r_mcangle_it 0.861 r_angle_other_deg 0.78 r_mcbond_it 0.436
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.824 r_dihedral_angle_4_deg 17.679 r_dihedral_angle_3_deg 13.001 r_dihedral_angle_1_deg 6.342 r_scangle_it 2.351 r_scbond_it 1.422 r_angle_refined_deg 1.243 r_mcangle_it 0.861 r_angle_other_deg 0.78 r_mcbond_it 0.436 r_mcbond_other 0.09 r_chiral_restr 0.076 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 2496 Nucleic Acid Atoms Solvent Atoms 320 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing