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Crystal structure of the phox homology domain of human phosphoinositide-3-kinase-C2-gamma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2AR5 PDB ENTRIES 2AR5, 2IWL,1O7K, 2V6V experimental model PDB 2IWL PDB ENTRIES 2AR5, 2IWL,1O7K, 2V6V experimental model PDB 1O7K PDB ENTRIES 2AR5, 2IWL,1O7K, 2V6V experimental model PDB 2V6V PDB ENTRIES 2AR5, 2IWL,1O7K, 2V6V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.5 0.1M TRI-SODIUM CITRATE DIHYDRATE PH 5.5, 20% PEG3000
Crystal Properties Matthews coefficient Solvent content 2.06 40.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.42 α = 90 b = 53.42 β = 90 c = 75.13 γ = 120
Symmetry Space Group P 32 2 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 MARRESEARCH 2009-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.25 29.16 99.9 0.07 16.8 8.6 34900 4.5 10
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 1.25 1.32 99.5 0.41 4.5 7.1
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 ENTRIES 2AR5, 2IWL,1O7K, 2V6V 1.25 26.71 33091 1772 99.83 0.16596 0.16502 0.1739 0.18398 0.1928 RANDOM 9.5
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 0.01 0.02 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.926 r_dihedral_angle_4_deg 13.613 r_dihedral_angle_3_deg 10.455 r_dihedral_angle_1_deg 5.148 r_scangle_it 3.514 r_scbond_it 2.165 r_angle_other_deg 1.631 r_mcangle_it 1.526 r_angle_refined_deg 1.282 r_mcbond_it 0.831
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.926 r_dihedral_angle_4_deg 13.613 r_dihedral_angle_3_deg 10.455 r_dihedral_angle_1_deg 5.148 r_scangle_it 3.514 r_scbond_it 2.165 r_angle_other_deg 1.631 r_mcangle_it 1.526 r_angle_refined_deg 1.282 r_mcbond_it 0.831 r_mcbond_other 0.205 r_chiral_restr 0.084 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 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 920 Nucleic Acid Atoms Solvent Atoms 175 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing