3NV7

Crystal structure of H.pylori phosphopantetheine adenylyltransferase mutant I4V/N76Y


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1H1T 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION5.529310% PEG 4000, 0.1M sodium acetate, 0.2M Li2SO4, pH 5.5, EVAPORATION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5451.54

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.022α = 90
b = 69.459β = 90
c = 95.92γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152008-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSRRC BEAMLINE BL13B11.0NSRRCBL13B1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.753018626
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8198.6

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 REPLACEMENTTHROUGHOUT1H1T1.7523.9817485941990.18960.18680.2414RANDOM31.2635
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]
0.030.01-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg14.359
r_dihedral_angle_1_deg5.305
r_scangle_it4.898
r_scbond_it3.452
r_mcangle_it2.442
r_mcbond_it1.536
r_angle_refined_deg1.332
r_nbtor_refined0.313
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.97
r_dihedral_angle_4_deg16.274
r_dihedral_angle_3_deg14.359
r_dihedral_angle_1_deg5.305
r_scangle_it4.898
r_scbond_it3.452
r_mcangle_it2.442
r_mcbond_it1.536
r_angle_refined_deg1.332
r_nbtor_refined0.313
r_nbd_refined0.218
r_symmetry_hbond_refined0.19
r_symmetry_vdw_refined0.186
r_xyhbond_nbd_refined0.139
r_chiral_restr0.092
r_bond_refined_d0.013
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1224
Nucleic Acid Atoms
Solvent Atoms136
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing