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Structure of the H258Y mutant of Phosphatidylinositol-specific phospholipase C from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V18 PDB ENTRY 3V18
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 4.6 293 26% PEG 4000,0.150M ammonium acetate,0.1M sodium acetate, 0.1M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.21 44.37
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.95 α = 90 b = 57.215 β = 90 c = 61.144 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++ 2011-09-28 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 1.9 50 98.1 0.093 156645 -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 1.9 1.93 80.2 4
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 3V18 1.9 34.87 24507 23280 1246 97.88 0.18927 0.18673 0.1842 0.23741 0.2359 RANDOM 27.048
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] 0.92 0.37 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.971 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_4_deg 14.019 r_dihedral_angle_1_deg 6.552 r_scangle_it 4.622 r_scbond_it 3.128 r_mcangle_it 2.147 r_angle_refined_deg 1.817 r_mcbond_it 1.257 r_chiral_restr 0.139
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.971 r_dihedral_angle_3_deg 14.182 r_dihedral_angle_4_deg 14.019 r_dihedral_angle_1_deg 6.552 r_scangle_it 4.622 r_scbond_it 3.128 r_mcangle_it 2.147 r_angle_refined_deg 1.817 r_mcbond_it 1.257 r_chiral_restr 0.139 r_bond_refined_d 0.023 r_gen_planes_refined 0.01 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 2455 Nucleic Acid Atoms Solvent Atoms 265 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement PHASER phasing CNS refinement HKL-2000 data reduction HKL-2000 data scaling HKL-2000 data collection