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Crystal structure of sigma-54 interaction domain of putative transcriptional response regulator from Neisseria gonorrhoeae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 289 0.17 M Ammonium acetate, 0.085 M Sodium citrate, 25.5% PEG 4000, 15% Glycerol, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.77 55.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.963 α = 90 b = 67.963 β = 90 c = 64.93 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 QUANTUM 315 2008-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97920 APS 19-ID
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 30.2 99.6 0.07 12.3 11.4 13120 13120 68
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 2.49 99.2 0.837 2.86 10.1 1312
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 (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 SAD THROUGHOUT 2.4 30.2 13111 13111 644 99.71 0.206 0.206 0.205 0.2079 0.241 0.2516 RANDOM 39.738
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] -0.03 -0.02 -0.03 0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_3_deg 19.536 r_dihedral_angle_4_deg 13.447 r_dihedral_angle_1_deg 7.381 r_scangle_it 3.143 r_scbond_it 2.121 r_angle_refined_deg 1.667 r_mcangle_it 1.278 r_angle_other_deg 1.065 r_mcbond_it 1.019
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.276 r_dihedral_angle_3_deg 19.536 r_dihedral_angle_4_deg 13.447 r_dihedral_angle_1_deg 7.381 r_scangle_it 3.143 r_scbond_it 2.121 r_angle_refined_deg 1.667 r_mcangle_it 1.278 r_angle_other_deg 1.065 r_mcbond_it 1.019 r_symmetry_vdw_other 0.394 r_symmetry_vdw_refined 0.322 r_nbd_refined 0.232 r_nbd_other 0.196 r_nbtor_refined 0.181 r_mcbond_other 0.166 r_xyhbond_nbd_refined 0.137 r_symmetry_hbond_refined 0.104 r_chiral_restr 0.094 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2031 Nucleic Acid Atoms Solvent Atoms 25 Heterogen Atoms 8
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction SHELXD phasing MLPHARE phasing DM phasing SOLVE phasing RESOLVE phasing HKL-3000 phasing