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Crystal structure of extragenic suppressor protein suhB from Bartonella henselae, via combined iodide SAD molecular replacement
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2QFL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 289 24 mg/mL protein in 0.2 M MgCl2, 0.1 M Hepes pH 7.5, 30% PEG 400 soaked into 0.2 M MgCl2, 0.75 M KI, 0.1 M Hepes pH 8.2, 35% PEG 400; crystal tracking ID for growth 206523d2 and 206575a1 for iodide soak, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 1.94 36.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.54 α = 90 b = 81.28 β = 98.78 c = 58.76 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+ 2010-01-13 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 2.05 30 96.7 0.066 18.26 7.3 27477 -3 38.09
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 2.05 2.1 82.1 0.439 4.2 5.9
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 SAD, MOLECULAR REPLACEMENT THROUGHOUT 2qfl 2.05 29.04 27458 1395 96.76 0.219 0.217 0.2164 0.262 0.2612 RANDOM 57.542
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] -0.77 -0.27 2.65 -1.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.204 r_dihedral_angle_3_deg 16.803 r_dihedral_angle_4_deg 16.274 r_dihedral_angle_1_deg 6.379 r_angle_refined_deg 1.472 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3508 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms 15
Software Software Software Name Purpose XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XDS data reduction