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Crystal Structure of capsular polysaccharide assembling protein CapF from staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZKL PDB entry 2ZKL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.1 293 300mM NaCl, 100mM ammonium sulfate, 100mM MES, 3.9M sodium formate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.53 α = 90 b = 119.53 β = 90 c = 129.45 γ = 120
Symmetry Space Group P 32 2 1
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 4 2007-04-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.000 Photon Factory BL-17A
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 2.45 103.52 99.8 0.07 0.07 20 8.9 39695 39695 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.45 2.58 100 0.858 0.858 0.91 0.302 0.9 9 5728
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 (All) 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 2ZKL 2.45 103.52 39636 39636 1597 99.68 0.1926 0.1926 0.1917 0.189 0.2141 0.2088 RANDOM 70.4644
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] -0.65 -0.33 -0.65 0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.377 r_dihedral_angle_4_deg 21.205 r_dihedral_angle_3_deg 19.956 r_dihedral_angle_1_deg 6.424 r_scangle_it 3.617 r_scbond_it 2.253 r_angle_refined_deg 1.465 r_mcangle_it 1.388 r_mcbond_it 0.702 r_chiral_restr 0.121
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.377 r_dihedral_angle_4_deg 21.205 r_dihedral_angle_3_deg 19.956 r_dihedral_angle_1_deg 6.424 r_scangle_it 3.617 r_scbond_it 2.253 r_angle_refined_deg 1.465 r_mcangle_it 1.388 r_mcbond_it 0.702 r_chiral_restr 0.121 r_bond_refined_d 0.012 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2987 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 13
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction SERGUI data collection