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Crystal structure of a TetR-like transcriptional regulator (Sama_0099) from Shewanella amazonensis SB2B at 2.42 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 277 0.4M KH2PO4, 1.6M NaH2PO4, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.76 67.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.536 α = 90 b = 123.536 β = 90 c = 49.552 γ = 90
Symmetry Space Group P 43 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 MARMOSAIC 325 mm CCD double crystal monochromator 2011-03-09 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91837,0.97934,0.97915 SSRL BL9-2
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 2.42 29.118 99.7 0.143 7.82 15161 -3 70.116
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 2.42 2.51 99.8 0.025 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.42 29.118 15113 762 99.74 0.2068 0.2047 0.1997 0.2496 0.2431 RANDOM 65.5524
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] -2.09 -2.09 4.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.754 r_dihedral_angle_4_deg 14.953 r_dihedral_angle_3_deg 13.638 r_scangle_it 9.652 r_scbond_it 6.911 r_mcangle_it 3.838 r_dihedral_angle_1_deg 2.991 r_mcbond_it 2.067 r_angle_refined_deg 1.724 r_angle_other_deg 1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.754 r_dihedral_angle_4_deg 14.953 r_dihedral_angle_3_deg 13.638 r_scangle_it 9.652 r_scbond_it 6.911 r_mcangle_it 3.838 r_dihedral_angle_1_deg 2.991 r_mcbond_it 2.067 r_angle_refined_deg 1.724 r_angle_other_deg 1.01 r_mcbond_other 0.475 r_chiral_restr 0.099 r_bond_refined_d 0.019 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1720 Nucleic Acid Atoms Solvent Atoms 38 Heterogen Atoms 54
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing