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Structure of a putative cAMP-binding regulatory protein from Silicibacter pomeroyi DSS-3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.49M NaH2PO4, 0.91M K2HPO4, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 3.27 62.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.728 α = 90 b = 137.728 β = 90 c = 94.626 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 CUSTOM-MADE 2007-12-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.97926,0.97940 APS 19-BM
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 2.2 50 99.7 0.079 35.955 7 33872 33872 -3 44.6
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 2.2 2.25 99.7 0.491 6.5 2284
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 MAD THROUGHOUT 2.2 31.54 33749 33749 1713 99.31 0.183 0.183 0.181 0.1937 0.218 0.2222 RANDOM 36.656
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] -1.26 -0.63 -1.26 1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.289 r_dihedral_angle_4_deg 19.959 r_dihedral_angle_3_deg 14.303 r_dihedral_angle_1_deg 5.784 r_scangle_it 3.862 r_scbond_it 2.414 r_angle_refined_deg 1.422 r_mcangle_it 1.396 r_angle_other_deg 0.882 r_mcbond_it 0.711
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.289 r_dihedral_angle_4_deg 19.959 r_dihedral_angle_3_deg 14.303 r_dihedral_angle_1_deg 5.784 r_scangle_it 3.862 r_scbond_it 2.414 r_angle_refined_deg 1.422 r_mcangle_it 1.396 r_angle_other_deg 0.882 r_mcbond_it 0.711 r_mcbond_other 0.182 r_chiral_restr 0.085 r_bond_refined_d 0.015 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 3464 Nucleic Acid Atoms Solvent Atoms 304 Heterogen Atoms 42
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MLPHARE phasing DM phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing SHELXD phasing SHELXE model building SOLVE phasing RESOLVE phasing ARP/wARP model building CCP4 phasing O model building Coot model building