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Periplasmic domain of the risS sensor protein from Burkholderia pesuromallei, low pH native structure
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LR0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 289 JCSG+ condition A6, 0.1 M phosphate-citrate pH 4.2, 0.2 M lithium sulfate, 25% PEG 1000, crystal tracking ID 208087a6, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.31 46.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.883 α = 90 b = 58.883 β = 90 c = 75.973 γ = 120
Symmetry Space Group P 32 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 ADSC QUANTUM 315r 2009-05-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.3 0.97650 ALS 5.0.3
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 2.1 30.46 98.5 0.07 13.2 13.7 9199
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 2.1 2.18 87.1 0.375 3.25 5.4 816
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT 3LR0 2.1 30.46 9175 439 98.41 0.183 0.181 0.1805 0.223 0.22 RANDOM 25.214
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] 0.38 0.19 0.38 -0.57
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.015 r_dihedral_angle_4_deg 21.242 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 6.244 r_scangle_it 4.109 r_scbond_it 2.373 r_mcangle_it 1.459 r_angle_refined_deg 1.355 r_mcbond_it 0.79 r_chiral_restr 0.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.015 r_dihedral_angle_4_deg 21.242 r_dihedral_angle_3_deg 13.237 r_dihedral_angle_1_deg 6.244 r_scangle_it 4.109 r_scbond_it 2.373 r_mcangle_it 1.459 r_angle_refined_deg 1.355 r_mcbond_it 0.79 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 911 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling