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Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IHY PDB ENTRIES 3IHY AND 1OIW experimental model PDB 1OIW PDB ENTRIES 3IHY AND 1OIW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.6 15% (W/V) PEG 4000, 0.1 M NA CITRATE PH 5.6, AND 0.2 M AMMONIUM ACETATE
Crystal Properties Matthews coefficient Solvent content 2.6 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.795 α = 90 b = 146.925 β = 90 c = 188.335 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 MARRESEARCH MIRRORS 2013-12-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 ESRF ID23-2
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 2.8 48.51 99.9 0.11 10.9 4.2 70875
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 2.8 2.86 99.9 1.04 1.1 4.3
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 3IHY AND 1OIW 2.94 115.84 58056 3095 99.54 0.21843 0.21626 0.2187 0.2594 0.2627 RANDOM 69.221
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] 6 0.74 -6.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.023 r_dihedral_angle_3_deg 18.591 r_dihedral_angle_4_deg 17.473 r_scangle_it 7.139 r_mcangle_it 6.6 r_dihedral_angle_1_deg 6.459 r_scbond_it 4.434 r_mcbond_it 4.172 r_mcbond_other 4.172 r_angle_refined_deg 1.49
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.023 r_dihedral_angle_3_deg 18.591 r_dihedral_angle_4_deg 17.473 r_scangle_it 7.139 r_mcangle_it 6.6 r_dihedral_angle_1_deg 6.459 r_scbond_it 4.434 r_mcbond_it 4.172 r_mcbond_other 4.172 r_angle_refined_deg 1.49 r_angle_other_deg 1.225 r_metal_ion_refined 0.305 r_xyhbond_nbd_other 0.304 r_symmetry_hbond_refined 0.298 r_xyhbond_nbd_refined 0.252 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.243 r_symmetry_vdw_other 0.236 r_nbd_other 0.213 r_nbtor_refined 0.191 r_nbtor_other 0.091 r_chiral_restr 0.081 r_symmetry_hbond_other 0.053 r_bond_refined_d 0.01 r_gen_planes_refined 0.007 r_bond_other_d 0.005 r_gen_planes_other 0.005 r_metal_ion_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 15675 Nucleic Acid Atoms Solvent Atoms 18 Heterogen Atoms 171
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing