3DF9

Crystal structure of E. coli MTA/SAH nucleosidase in complex with BnT-DADMeImmA


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Y6Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.529835 % (v/v) 2-propanol, 50 mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.2645.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.611α = 90
b = 69.748β = 90
c = 127.868γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-07-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

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
11.9563.9396.80.07824.615.9344753337255
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)
1.952.0295.30.39.815.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1Y6Q1.9563.893272031666168396.780.177150.177150.175480.20802RANDOM17.654
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]
0.52-0.16-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.993
r_dihedral_angle_4_deg13.772
r_dihedral_angle_3_deg12.78
r_dihedral_angle_1_deg5.98
r_scangle_it2.98
r_scbond_it1.812
r_angle_refined_deg1.308
r_mcangle_it1.071
r_mcbond_it0.576
r_chiral_restr0.084
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.993
r_dihedral_angle_4_deg13.772
r_dihedral_angle_3_deg12.78
r_dihedral_angle_1_deg5.98
r_scangle_it2.98
r_scbond_it1.812
r_angle_refined_deg1.308
r_mcangle_it1.071
r_mcbond_it0.576
r_chiral_restr0.084
r_bond_refined_d0.012
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3497
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms52

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing