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Calcium-dependent phosphoinositol-specific phospholipase C from a Gram-negative bacterium, Pseudomonas sp, apo form, crystal form 2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FYO PDB ENTRY 5FYO
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 1.97 37.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 135.21 α = 90 b = 135.21 β = 90 c = 112.47 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 2014-10-02 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 1.17 67.61 99.9 0.08 17.2 11.7 346088 2
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 5FYO 1.17 67.61 328719 17243 99.94 0.12594 0.1248 0.1371 0.1476 0.1561 RANDOM 12.925
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.003 r_dihedral_angle_2_deg 35.01 r_rigid_bond_restr 22.483 r_dihedral_angle_4_deg 16.249 r_dihedral_angle_3_deg 11.188 r_sphericity_bonded 11.103 r_dihedral_angle_1_deg 6.309 r_long_range_B_refined 4.852 r_long_range_B_other 4.679 r_scangle_other 3.168
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 39.003 r_dihedral_angle_2_deg 35.01 r_rigid_bond_restr 22.483 r_dihedral_angle_4_deg 16.249 r_dihedral_angle_3_deg 11.188 r_sphericity_bonded 11.103 r_dihedral_angle_1_deg 6.309 r_long_range_B_refined 4.852 r_long_range_B_other 4.679 r_scangle_other 3.168 r_scbond_it 2.781 r_scbond_other 2.781 r_angle_other_deg 2.153 r_mcangle_other 1.873 r_mcangle_it 1.872 r_mcbond_it 1.706 r_mcbond_other 1.704 r_angle_refined_deg 1.552 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.009 r_gen_planes_other 0.008 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 9131 Nucleic Acid Atoms Solvent Atoms 1843 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling MOLREP phasing