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Crystal structure of a putative transcriptional repressor of ribose operon from Staphylococcus saprophyticus subsp. saprophyticus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7 294 3M sodium formate, 275mM sodium thiocyanate, pH 7.0, Vapor diffusion, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.18 43.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.146 α = 90 b = 106.634 β = 112.17 c = 68.183 γ = 90
Symmetry Space Group C 1 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 MAR CCD 165 mm 2008-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97958 APS 31-ID
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 19.749 99.7 0.103 0.103 12.3 5.1 36225 36116 28.1
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 2 2.11 99.4 0.587 0.587 2.8 5.1 5227
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2 19.749 36225 36098 1842 99.65 0.214 0.212 0.2122 0.259 0.2565 RANDOM 39.625
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] -1.78 0.03 1.62 0.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.528 r_dihedral_angle_4_deg 22.713 r_dihedral_angle_3_deg 16.631 r_dihedral_angle_1_deg 5.978 r_scangle_it 3.925 r_scbond_it 2.656 r_mcangle_it 1.65 r_angle_refined_deg 1.542 r_mcbond_it 1.012 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.528 r_dihedral_angle_4_deg 22.713 r_dihedral_angle_3_deg 16.631 r_dihedral_angle_1_deg 5.978 r_scangle_it 3.925 r_scbond_it 2.656 r_mcangle_it 1.65 r_angle_refined_deg 1.542 r_mcbond_it 1.012 r_nbtor_refined 0.312 r_symmetry_hbond_refined 0.298 r_symmetry_vdw_refined 0.277 r_nbd_refined 0.219 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.111 r_bond_refined_d 0.016 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3691 Nucleic Acid Atoms Solvent Atoms 119 Heterogen Atoms 12
Software Software Software Name Purpose SCALA data scaling REFMAC refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SHELXCD phasing SHELXE model building