1Q6Y

Hypothetical protein YfdW from E. coli bound to Coenzyme A


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529865% MPD, 0.1 M Bis-Tris pH 6.5, 1.5 mM CoA, 1.5 mM oxalate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2545.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 92.117α = 90
b = 66.779β = 108.73
c = 73.049γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCH2003-06-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.992093.60.06610.53.42708227082-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0772.30.26552.22082

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1pqy1.9919.78-325765131793.530.170.160.2random
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
o_angle_deg2
o_bond_d0.02
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
RMS Deviations
KeyRefinement Restraint Deviation
o_angle_deg2
o_bond_d0.02
o_bond_d_na
o_bond_d_prot
o_angle_d
o_angle_d_na
o_angle_d_prot
o_angle_deg_na
o_angle_deg_prot
o_dihedral_angle_d
o_dihedral_angle_d_na
o_dihedral_angle_d_prot
o_improper_angle_d
o_improper_angle_d_na
o_improper_angle_d_prot
o_mcbond_it
o_mcangle_it
o_scbond_it
o_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3200
Nucleic Acid Atoms
Solvent Atoms276
Heterogen Atoms97

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
REFMACrefinement
CNSphasing