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A covalent S-F heterodimer of staphylococcal gamma-hemolysin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LKF pdb entries 1LKF, 1T5R experimental model PDB 1T5R pdb entries 1LKF, 1T5R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 285 covalent complex concentrated to 9 mg/ml in 50 mM MES-NaOH, 50 mM NaCl, pH 6.5. Needle and rod shape like crystals obtained in drops prepared by mixing two volumes of protein and one volume of reservoir solution containing 10% polyethylene glycol 8000, 0.05 M Na citrate, pH 5.5. Reservoir volumes of 500 mul used, VAPOR DIFFUSION, SITTING DROP, temperature 285K
Crystal Properties Matthews coefficient Solvent content 3.06 59.78
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 140 α = 90 b = 140 β = 90 c = 73.078 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 2005-02-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.9330 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.4 50.5 100 0.078 8 7 32122 32122
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.318 2.3 6.6
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 entries 1LKF, 1T5R 2.4 30 30458 1625 100 0.1825 0.17953 0.1848 0.2388 0.2423 RANDOM 46.121
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] 0.4 0.2 0.4 -0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.239 r_dihedral_angle_3_deg 17.366 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_1_deg 7.849 r_scangle_it 4.861 r_scbond_it 3.301 r_mcangle_it 2.153 r_angle_refined_deg 2.028 r_mcbond_it 1.257 r_nbtor_refined 0.318
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.239 r_dihedral_angle_3_deg 17.366 r_dihedral_angle_4_deg 17.234 r_dihedral_angle_1_deg 7.849 r_scangle_it 4.861 r_scbond_it 3.301 r_mcangle_it 2.153 r_angle_refined_deg 2.028 r_mcbond_it 1.257 r_nbtor_refined 0.318 r_nbd_refined 0.225 r_symmetry_vdw_refined 0.172 r_xyhbond_nbd_refined 0.154 r_chiral_restr 0.135 r_symmetry_hbond_refined 0.135 r_bond_refined_d 0.024 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 4303 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction SCALA data scaling MOLREP phasing PHASER phasing