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An intramolecular pi-cation latch in phosphatidylinositol-specific phospholipase C from S.aureus controls substrate access to the active site
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1PTG PDB entry 1PTG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 20% PEG 4000, 0.15 M ammonium acetate, 0.1 M sodium acetate, 0.01M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 40.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.161 α = 90 b = 43.607 β = 90 c = 62.218 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 120 IMAGE PLATE RIGAKU RAXIS IV++ Osmic VariMax 2011-03-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 2.05 50 97.5 0.045 12.3 18544 18080 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.09 77.5 6
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1PTG 2.05 39.94 13127 17112 923 97.4 0.15844 0.15552 0.1569 0.21314 0.209 RANDOM 28.493
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] -0.66 -0.5 1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.175 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_1_deg 6.696 r_scangle_it 4.981 r_dihedral_angle_4_deg 4.492 r_scbond_it 3.25 r_mcangle_it 1.962 r_angle_refined_deg 1.755 r_mcbond_it 1.124 r_chiral_restr 0.123
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.175 r_dihedral_angle_3_deg 15.181 r_dihedral_angle_1_deg 6.696 r_scangle_it 4.981 r_dihedral_angle_4_deg 4.492 r_scbond_it 3.25 r_mcangle_it 1.962 r_angle_refined_deg 1.755 r_mcbond_it 1.124 r_chiral_restr 0.123 r_bond_refined_d 0.022 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2418 Nucleic Acid Atoms Solvent Atoms 225 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling CrystalClear data collection