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The structure of a putative signal-transduction protein with CBS domains from Burkholderia ambifaria MC40-6
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RC3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 298 40.6 mg/ml BuamA.00062.b.A1.PS01259, 20% PEG 3350, 200mM potassium nitrate, cryo protection 20% PEG 300, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 33.35 α = 90 b = 56.63 β = 98.41 c = 76.58 γ = 90
Symmetry Space Group P 1 21 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 RIGAKU SATURN 944+ 2012-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.5418
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 31.485 97.9 0.073 9.8 16262 -3 39.773
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 2.15 90.6 0.381 2.68
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 2RC3 2.1 16262 819 97.85 0.2252 0.2229 0.2236 0.2669 0.2588 RANDOM 40.103
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] -1.79 -1.53 2.15 -0.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.809 r_dihedral_angle_3_deg 14.577 r_dihedral_angle_4_deg 10.256 r_dihedral_angle_1_deg 5.589 r_angle_refined_deg 1.563 r_angle_other_deg 0.887 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.809 r_dihedral_angle_3_deg 14.577 r_dihedral_angle_4_deg 10.256 r_dihedral_angle_1_deg 5.589 r_angle_refined_deg 1.563 r_angle_other_deg 0.887 r_chiral_restr 0.062 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1953 Nucleic Acid Atoms Solvent Atoms 49 Heterogen Atoms 134
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction