3LUZ

Crystal structure of extragenic suppressor protein suhB from Bartonella henselae, via combined iodide SAD molecular replacement


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QFL 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.528924 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 coefficientSolvent content
1.9436.72

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.54α = 90
b = 81.28β = 98.78
c = 58.76γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-01-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.053096.70.06618.267.327477-338.09
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.182.10.4394.25.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSAD, MOLECULAR REPLACEMENTTHROUGHOUT2qfl2.0529.0427458139596.760.2190.2170.262RANDOM57.542
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]
-0.77-0.272.65-1.97
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.204
r_dihedral_angle_3_deg16.803
r_dihedral_angle_4_deg16.274
r_dihedral_angle_1_deg6.379
r_angle_refined_deg1.472
r_chiral_restr0.091
r_bond_refined_d0.014
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3508
Nucleic Acid Atoms
Solvent Atoms124
Heterogen Atoms15

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction