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Structure of the Y250A mutant of the PANTON-VALENTINE LEUCOCIDIN S component from STAPHYLOCOCCUS AUREUS
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1T5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 285 5% PEG 6000, 0.1M NaCitrate , pH 4.00, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 2.2 44.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.34 α = 90 b = 89.32 β = 90 c = 38.1 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 ADSC QUANTUM 315r 2008-11-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.94800 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 30.84 99.7 0.067 0.067 18.8 6.9 43049 43049 18.72
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 1.6 99.9 0.753 0.753 3.2 5.7 3855
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1T5R 1.55 22.69 43037 2161 99.75 0.1665 0.1653 0.1893 0.1918 RANDOM 22.36
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] -1.1181 4.0269 -2.9089
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.45 t_omega_torsion 4.37 t_angle_deg 1.06 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 15.45 t_omega_torsion 4.37 t_angle_deg 1.06 t_bond_d 0.009 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2242 Nucleic Acid Atoms Solvent Atoms 297 Heterogen Atoms 30
Software Software Software Name Purpose DNA data collection PHASER phasing BUSTER refinement XDS data reduction XSCALE data scaling