3NBK

Phosphopantetheine Adenylyltransferase from Mycobacterium tuberculosis in complex with 4'-phosphopantetheine


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TFUPDB entry 1TFU

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP72940.05 M Hepes pH 7 and 2.5 v/v % isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
3.5164.92

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.627α = 90
b = 114.627β = 90
c = 135.206γ = 120
Symmetry
Space GroupP 3 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77CCDMARMOSAIC 225 mm CCD2009-08-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 22-BM1.0APS22-BM

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
11.58135.2199.90.09432.910.5141372141259223.3
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)
1.581.6199.90.6663.48.67008

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 REPLACEMENTTHROUGHOUTPDB entry 1TFU1.58135.21134177708299.920.184080.183280.19906RANDOM18.483
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]
-0.29-0.15-0.290.44
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.82
r_dihedral_angle_4_deg12.256
r_dihedral_angle_3_deg11.323
r_dihedral_angle_1_deg4.878
r_scangle_it3.408
r_scbond_it2.027
r_mcangle_it1.35
r_angle_refined_deg1.241
r_mcbond_it0.714
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.82
r_dihedral_angle_4_deg12.256
r_dihedral_angle_3_deg11.323
r_dihedral_angle_1_deg4.878
r_scangle_it3.408
r_scbond_it2.027
r_mcangle_it1.35
r_angle_refined_deg1.241
r_mcbond_it0.714
r_chiral_restr0.083
r_bond_refined_d0.009
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4903
Nucleic Acid Atoms
Solvent Atoms775
Heterogen Atoms90

Software

Software
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling