4MB6

Crystal structure of adenine phosphoribosyltransferase from Yersinia pseudotuberculosis.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2DY0PDB ENTRY 2DY0

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72982.4M sodium malonate pH 7.0, Vapor diffusion, Sitting drop, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.8356.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.56α = 90
b = 78.38β = 112.98
c = 54.01γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152013-07-18SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.978NSLSX29A

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
11.80749.72499.20.04718.46204292042932
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.811.999.10.4650.4651.65.92947

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2DY01.8140.192042820428104099.10.18680.1840.2382RANDOM43.9246
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]
0.80.75-0.36-0.55
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.206
r_dihedral_angle_4_deg24.533
r_dihedral_angle_3_deg14.682
r_dihedral_angle_1_deg6.173
r_mcangle_it3.514
r_mcbond_it2.611
r_mcbond_other2.61
r_angle_refined_deg1.971
r_angle_other_deg0.894
r_chiral_restr0.121
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.206
r_dihedral_angle_4_deg24.533
r_dihedral_angle_3_deg14.682
r_dihedral_angle_1_deg6.173
r_mcangle_it3.514
r_mcbond_it2.611
r_mcbond_other2.61
r_angle_refined_deg1.971
r_angle_other_deg0.894
r_chiral_restr0.121
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1391
Nucleic Acid Atoms
Solvent Atoms31
Heterogen Atoms1

Software

Software
Software NamePurpose
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
MOSFLMdata reduction