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Crystal structure of human SHIP2 in complex with biphenyl 2,3',4,5',6- pentakisphosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NR8 PDB ENTRY 3NR8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 1.5 MM BIPHENYL 2,3,4,5, 6-PENTAKISPHOSPHATE, 2 MM MGSO4, 11% PEG 6000, 0.1 M CITRIC ACID PH 4.8
Crystal Properties Matthews coefficient Solvent content 2.2 44.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.246 α = 90 b = 61.52 β = 91.94 c = 114.742 γ = 90
Symmetry Space Group P 1 21 1
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 ADSC CCD 2010-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 2.1 45.22 99 0.07 8.6 3.8 36559 -3 37.61
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 2.1 2.21 98.4 0.61 1.2 3.8
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 PDB ENTRY 3NR8 2.1 29.41 36540 1787 98.74 0.2019 0.2009 0.2123 0.221 0.2368 RANDOM 46.48
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] 0.2514 2.9253 5.0585 0.8071
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.91 t_omega_torsion 2.36 t_angle_deg 0.9 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 2.91 t_omega_torsion 2.36 t_angle_deg 0.9 t_bond_d 0.008 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4686 Nucleic Acid Atoms Solvent Atoms 252 Heterogen Atoms 37
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PHASER phasing