5JVO

Crystal structure of the Arginine Repressor from the pathogenic bacterium Corynebacterium pseudotuberculosis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ERE 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5291100 mM Tris-HCl 200 mM NaCl 10% ethanol
Crystal Properties
Matthews coefficientSolvent content
2.2645.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.191α = 90
b = 83.191β = 90
c = 83.191γ = 90
Symmetry
Space GroupP 21 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M2015-05-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.458LNLSW01B-MX2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.94899.90.0790.99920.8110.515299-336.141
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)
11.92.0299.50.8992.15

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3ERE1.9481453376499.950.18190.17970.2249RANDOM34.866
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.339
r_dihedral_angle_4_deg20.664
r_dihedral_angle_3_deg17.714
r_dihedral_angle_1_deg6.793
r_mcangle_it3.347
r_mcbond_other2.415
r_mcbond_it2.414
r_angle_refined_deg2.372
r_angle_other_deg1.157
r_chiral_restr0.145
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.339
r_dihedral_angle_4_deg20.664
r_dihedral_angle_3_deg17.714
r_dihedral_angle_1_deg6.793
r_mcangle_it3.347
r_mcbond_other2.415
r_mcbond_it2.414
r_angle_refined_deg2.372
r_angle_other_deg1.157
r_chiral_restr0.145
r_bond_refined_d0.026
r_gen_planes_refined0.013
r_bond_other_d0.002
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1158
Nucleic Acid Atoms
Solvent Atoms46
Heterogen Atoms31

Software

Software
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing