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Crystal structure of human SHIP2 Phosphatase-C2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 293 0.1 M BisTris propane pH 7, 0.2 M NaNO3, 20% PEG 3350, 0.025% CH2Cl2, 2 mM TCEP
Crystal Properties Matthews coefficient Solvent content 2.54 51.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 136.037 α = 90 b = 175.836 β = 90 c = 176.893 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 PIXEL DECTRIS PILATUS 6M 2012-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.976 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rpim I (All) CC (Half) 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 1.96 48.97 100 0.033 0.999 14.8 6.8 287002
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.96 1.99 100 0.368 0.743 2.1 6.7
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 3NR8 1.96 48.96 287002 15180 99.97 0.18091 0.1795 0.1875 0.2075 0.2131 RANDOM 45.654
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] -1.12 -0.15 1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 19.696 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.198 r_long_range_B_refined 5.622 r_long_range_B_other 5.614 r_mcangle_it 2.42 r_mcangle_other 2.42 r_scangle_other 2.362 r_mcbond_it 1.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.215 r_dihedral_angle_4_deg 19.696 r_dihedral_angle_3_deg 13.663 r_dihedral_angle_1_deg 6.198 r_long_range_B_refined 5.622 r_long_range_B_other 5.614 r_mcangle_it 2.42 r_mcangle_other 2.42 r_scangle_other 2.362 r_mcbond_it 1.38 r_mcbond_other 1.38 r_scbond_it 1.346 r_scbond_other 1.346 r_angle_refined_deg 1.306 r_angle_other_deg 1.241 r_chiral_restr 0.077 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 28047 Nucleic Acid Atoms Solvent Atoms 1564 Heterogen Atoms 225
Software Software Software Name Purpose REFMAC refinement XDS data reduction SCALA data scaling PHASER phasing