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Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, myoinositol complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FYP PDB ENTRY 5FYP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 10 PEG3350 24-27%, CAPS/BICINE MIX PH 9.0-10 GRID, BEST CRYSTALS CLOSER TO PH 10, SEEDING FROM PACT H4 (0.2M KSCN, 20% PEG3350, BIS TRIS PROPANE PH 8.5), ORYX ROBOT, 24 WELL PLATE, HANGING DROPS
Crystal Properties Matthews coefficient Solvent content 1.99 38.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.443 α = 90 b = 135.443 β = 90 c = 113.732 γ = 90
Symmetry Space Group P 43 21 2
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 PILATUS3 6M 2015-05-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.45 48.93 99.7 0.07 14.5 7.2 184175 2
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 1.45 1.47 95.2 0.6 2.5 5.7
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 PDB ENTRY 5FYP 1.45 48.93 174938 9159 99.68 0.14722 0.14488 0.1586 0.19184 0.2015 RANDOM 16.818
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] -0.07 -0.07 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.774 r_sphericity_free 27.31 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 11.608 r_sphericity_bonded 9.027 r_dihedral_angle_1_deg 6.327 r_rigid_bond_restr 4.143 r_long_range_B_refined 3.962 r_long_range_B_other 3.925 r_scangle_other 3.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.774 r_sphericity_free 27.31 r_dihedral_angle_4_deg 16.4 r_dihedral_angle_3_deg 11.608 r_sphericity_bonded 9.027 r_dihedral_angle_1_deg 6.327 r_rigid_bond_restr 4.143 r_long_range_B_refined 3.962 r_long_range_B_other 3.925 r_scangle_other 3.216 r_scbond_it 2.708 r_scbond_other 2.708 r_mcangle_other 2.146 r_mcangle_it 2.145 r_mcbond_it 1.877 r_mcbond_other 1.876 r_angle_refined_deg 1.666 r_angle_other_deg 1.101 r_chiral_restr 0.468 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.003 r_bond_other_d 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9065 Nucleic Acid Atoms Solvent Atoms 1072 Heterogen Atoms 67
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing