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Structure of a Ca+2 dependent Phosphatidylinositol-specific phospholipase C (PI-PLC) Enzyme from Streptomyces antibioticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 277 21% PEG 10000, 85mM sodium acetate pH 4.6, 170mM ammonium acetate, 9% glycerol. SeMe-derived crystals obtained with initial microseeding with underivatized crystals followed by a series of macroseedings with derivatized enzyme and same conditions., VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.28 46.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.377 α = 90 b = 155.172 β = 90 c = 41.409 γ = 90
Symmetry Space Group P 21 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 CCD MARMOSAIC 325 mm CCD 2008-01-01 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9796 SSRL BL9-2
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 1.5 77.61 95.15 0.058 8.2689 11.65 52173 52171 3.7 13.6
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) 1.5 1.58 81.66 0.22 3.19 5.76 6345
Refinement Statistics Diffraction ID Structure Solution Method 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 SAD 1.5 77.59 52168 5234 94.73 0.185 0.184 0.1758 0.2 0.1928 RANDOM 14.295
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] 1.12 -0.61 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.275 r_dihedral_angle_4_deg 11.859 r_dihedral_angle_3_deg 10.883 r_dihedral_angle_1_deg 5.111 r_sphericity_free 2.344 r_scangle_it 2.19 r_sphericity_bonded 1.674 r_scbond_it 1.591 r_angle_refined_deg 0.995 r_mcangle_it 0.981
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.275 r_dihedral_angle_4_deg 11.859 r_dihedral_angle_3_deg 10.883 r_dihedral_angle_1_deg 5.111 r_sphericity_free 2.344 r_scangle_it 2.19 r_sphericity_bonded 1.674 r_scbond_it 1.591 r_angle_refined_deg 0.995 r_mcangle_it 0.981 r_rigid_bond_restr 0.877 r_mcbond_it 0.567 r_chiral_restr 0.068 r_bond_refined_d 0.005 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2411 Nucleic Acid Atoms Solvent Atoms 314 Heterogen Atoms 49
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling SHELX phasing REFMAC refinement PDB_EXTRACT data extraction SHELXD phasing