4TNN

Crystal structure of Escherichia coli protein YodA in complex with Ni - artifact of purification.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OEJ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72890.3 ul of 9.6 mg/ml protein in 50mM Tris pH 7.9, 300 mM NaCl and 0.5mM TCEP were mixed with 0.3 ul of the SaltRx condition #65 (2.5 M Ammonium sulfate, 0.1 M BIS-TRIS propane pH 7.0) and equilibrated against 1.5 M NaCl in MRC 2 drops 96 Well Crystallization Plate (Swissci)
Crystal Properties
Matthews coefficientSolvent content
2.3447.52

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.583α = 90
b = 76.583β = 90
c = 61.944γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCD2013-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.978APS21-ID-G

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.955099.90.080.0897.31564715635-328.4
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)
11.951.981000.7672.417.4750

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 REPLACEMENTTHROUGHOUT1OEJ1.951501561678299.940.16890.16660.2154RANDOM36.632
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]
0.20.10.2-0.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.206
r_dihedral_angle_4_deg15.162
r_dihedral_angle_3_deg14.378
r_dihedral_angle_1_deg6.492
r_mcangle_it2.02
r_angle_refined_deg1.5
r_mcbond_other1.417
r_mcbond_it1.416
r_angle_other_deg0.772
r_chiral_restr0.085
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.206
r_dihedral_angle_4_deg15.162
r_dihedral_angle_3_deg14.378
r_dihedral_angle_1_deg6.492
r_mcangle_it2.02
r_angle_refined_deg1.5
r_mcbond_other1.417
r_mcbond_it1.416
r_angle_other_deg0.772
r_chiral_restr0.085
r_bond_refined_d0.013
r_gen_planes_refined0.008
r_bond_other_d0.006
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1546
Nucleic Acid Atoms
Solvent Atoms137
Heterogen Atoms31

Software

Software
Software NamePurpose
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDEphasing
MLPHAREphasing
DMphasing
Cootmodel building
PDB_EXTRACTdata extraction
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling