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Structure of the global transcription regulator FapR from Staphylococcus aureus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2F3X PDB ENTRY 2F3X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.4 6% PEG-8000, 0.1M MES, 0.2 M ZN ACETATE, PH 5.4
Crystal Properties Matthews coefficient Solvent content 3.8 67
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 116.58 α = 90 b = 116.58 β = 90 c = 123.23 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 CCD ADSC CCD 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.4 47 99.9 0.06 15.6 5.5 12145
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.53 100 0.63 2.5 5.6
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 ENTRY 2F3X 2.4 78.09 12145 623 99.87 0.19867 0.19643 0.2052 0.24617 0.2512 RANDOM 63.009
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] -0.83 -0.42 -0.83 1.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.477 r_dihedral_angle_4_deg 19.547 r_dihedral_angle_3_deg 15.301 r_dihedral_angle_1_deg 5.922 r_scangle_it 2.326 r_angle_refined_deg 1.638 r_scbond_it 1.457 r_mcangle_it 0.873 r_mcbond_it 0.449 r_chiral_restr 0.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.477 r_dihedral_angle_4_deg 19.547 r_dihedral_angle_3_deg 15.301 r_dihedral_angle_1_deg 5.922 r_scangle_it 2.326 r_angle_refined_deg 1.638 r_scbond_it 1.457 r_mcangle_it 0.873 r_mcbond_it 0.449 r_chiral_restr 0.17 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1460 Nucleic Acid Atoms Solvent Atoms 20 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling AMoRE phasing