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Structure of the C-terminal domains of a LysR family protein from Agrobacterium tumefaciens str. C58.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.6 295 0.1M sodium citrate pH5.6, 0.1M ammonium acetate, 15% PEG 4000, 1/800 (w/w) endoproteinase Glu-C V8, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.99 58.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.613 α = 90 b = 53.613 β = 90 c = 188.027 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 ADSC QUANTUM 315 2008-08-07 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97935,0.97948 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 1.7 50 98.3 0.074 51 14.8 30842 30842 -3 25.6
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 1.7 1.73 78.4 0.405 10.2 1235
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 1.7 37.16 30737 30737 1550 98.2 0.171 0.171 0.169 0.1777 0.2 0.209 RANDOM 26.747
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] 1.49 1.49 -2.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.188 r_dihedral_angle_4_deg 21.629 r_dihedral_angle_3_deg 12.793 r_dihedral_angle_1_deg 5.874 r_scangle_it 3.503 r_scbond_it 2.234 r_mcangle_it 1.389 r_angle_refined_deg 1.381 r_angle_other_deg 0.831 r_mcbond_it 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.188 r_dihedral_angle_4_deg 21.629 r_dihedral_angle_3_deg 12.793 r_dihedral_angle_1_deg 5.874 r_scangle_it 3.503 r_scbond_it 2.234 r_mcangle_it 1.389 r_angle_refined_deg 1.381 r_angle_other_deg 0.831 r_mcbond_it 0.76 r_mcbond_other 0.218 r_chiral_restr 0.081 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1572 Nucleic Acid Atoms Solvent Atoms 236 Heterogen Atoms 40
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